My MK3 does not rev beyond 4500rpm

After inspecting the Gearbox to chassis assembly I discover the thick upper washer was installed on the left hand side between the gearbox and the chassis instead of the right hand side. This made the gearbox main-shaft to be tilted down instead of perfectly aligned with the crankshaft.
The first picture is with the gearbox wrongly installed in the chassis while on the second one I properly installed it:



The result is the primary chain has been rubbing the transmission case inner perimeter and also the chain hidraulic tensioner steel plate. For me it is clear this high friction was reducing power from the engine and preventing it to rev.
Here the pictures of the transmission case in which are visible the marks left on the aluminum as a result of friction.



Fortunately the primary chain, crankshaft sprocket and clutch chainwheel have not visible damage and the tensioner plate although remarkably marked it has not damage on relevant parts therefore I can just assemble everything properly with new oil seals, and gaskets.
I have seen the gearbox sprocket installed is a 22T in perfect shape but know that it is easy I will order a 20T and a new 530 pitch 99 links drive chain to get more acceleration on the back roads I normally ride.

Do you suggest to order/adjust or consider any further updates to finally make the engine run and rev properly?
 
After inspecting the Gearbox to chassis assembly I discover the thick upper washer was installed on the left hand side between the gearbox and the chassis instead of the right hand side.
It should be on the left side.
 
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Surely you must have heard the noise coming from your primary case with the rubbing of the chain on the case as they are deep wear marks.
 
Sorry I made a mistake writing! I mean I found the thick washer installed on the Right side whereas it should have been on the Left side.
I have already installed it properly on the Left side and torqed first the upper nut at 55 lbs/pound and then the bottom one also at 55 lbs/pound.
 
After inspecting the Gearbox to chassis assembly I discover the thick upper washer was installed on the left hand side between the gearbox and the chassis instead of the right hand side. This made the gearbox main-shaft to be tilted down instead of perfectly aligned with the crankshaft.
The first picture is with the gearbox wrongly installed in the chassis while on the second one I properly installed it:



The result is the primary chain has been rubbing the transmission case inner perimeter and also the chain hidraulic tensioner steel plate. For me it is clear this high friction was reducing power from the engine and preventing it to rev.
Here the pictures of the transmission case in which are visible the marks left on the aluminum as a result of friction.



Fortunately the primary chain, crankshaft sprocket and clutch chainwheel have not visible damage and the tensioner plate although remarkably marked it has not damage on relevant parts therefore I can just assemble everything properly with new oil seals, and gaskets.
I have seen the gearbox sprocket installed is a 22T in perfect shape but know that it is easy I will order a 20T and a new 530 pitch 99 links drive chain to get more acceleration on the back roads I normally ride.

Do you suggest to order/adjust or consider any further updates to finally make the engine run and rev properly?

I'm sorry but I can't see anything here that'd stop the bike from revving beyond 4500 rpm
 
I'm sorry but I can't see anything here that'd stop the bike from revving beyond 4500 rpm
Ya, I probably missed it in 185 posts, way back in #118 @MexicoMike asked: "will it rev past 4500 in neutral?" I'm still hoping to hear that answer and sorry if I missed it! Just about every possible problem on a Command has been discussed and still haven't got a clear problem to fix. Fixing symptoms is a fools errand, IMHO.

The gearbox spacer was a problem, but I've come across quite a few where the spacer was left out and the cradle is warped - not heard of it causing a reving problem but then this is a MK3 so could be different.
 
At the beggining when in neutral the engine was able to rev up to 6000rpm but no more.
The fact is that due to the wrong gearbox to chassis installation the primary transmission chain was rubbing on the case and to my understanding this high friction was reducing power to the engine and probably not letting it rev.
In fact the friction increased the more I drived the bike and finally the engine was not able to idle and stopped. I tried to started up and there was a lot of friction using the kick starter pedal.

If you consider I should check out anything else I am ready to do it.
As a resume of the post I made the following to the bike:
ELECTRICS
-New Lucas individual coils with leads, caps and Champion N7Y spark plugs.
-New Boyer MKIV electronics Ignition
-New negative earth wiring with Motogadget M-unit electronic sistem
-New STATOR THREE PHASE (WASSELL) Alternador Lucas WW10192L 12V, 14,5 Amp High Output
-New SOLID STATE POWERBOX REPLACES RECTIFIER & ZENER DIODE, SUITABLE FOR 3 PHASE

ENGINE
-Refurbished head with new valve seals with new head gasket
-Refurbished barrels with new rings
-Revised and properly adjusted timing chain and camshaft sprocket
-PCV BREATHER CRANKCASE VACUUM NON RETURN VALVE
-Oil pressure gauge
-Refurbished oil pump
-New Triplex primary chain
-New STARTER SPRAG BEARING CLUTCH
-New HYDRAULIC TENSIONER PAD, PISTON AND SPRING
-New Barnett clutch plates KIT
-New AMAL PREMIER 932 Carburetors with 260 Main jet, 106 throttle jet, 3 1/2" throttle slide cutaway and 19 removable pilot jet.
-New K&N single open air filter without air filter box
-New open peashooter style silencers with new unbalanced pipes

-Rebuilt GEARBOX with new oil seals and KICKSTART SHAFT BUSH

The bike has been completely rebuilt from scratch including brakes, brake pumps, new disc brakes, refurbished wheels, fork with Lansdowne Dampers, new Ikon shocks.

The only part I have not done myself for it was already refurbished by the man that sold me the bike is the engine case with the camshaft but I properly adjusted the timing.
 
"Refurbished head with new valve seals with new head gasket" - seals and a gasket is not considered refurbishment of the head. Or did you do other things with the head?
 
After inspecting the Gearbox to chassis assembly I discover the thick upper washer was installed on the left hand side between the gearbox and the chassis instead of the right hand side. This made the gearbox main-shaft to be tilted down instead of perfectly aligned with the crankshaft.
The first picture is with the gearbox wrongly installed in the chassis while on the second one I properly installed it:



The result is the primary chain has been rubbing the transmission case inner perimeter and also the chain hidraulic tensioner steel plate. For me it is clear this high friction was reducing power from the engine and preventing it to rev.
Here the pictures of the transmission case in which are visible the marks left on the aluminum as a result of friction.



Fortunately the primary chain, crankshaft sprocket and clutch chainwheel have not visible damage and the tensioner plate although remarkably marked it has not damage on relevant parts therefore I can just assemble everything properly with new oil seals, and gaskets.
I have seen the gearbox sprocket installed is a 22T in perfect shape but know that it is easy I will order a 20T and a new 530 pitch 99 links drive chain to get more acceleration on the back roads I normally ride.

Do you suggest to order/adjust or consider any further updates to finally make the engine run and rev properly?

I had this issue on my mk2 bike...a shop that reassembled the primary case and installed the gearbox did not use the correct thick washer/spacer between gearbox and right hand engine cradle plate. It did not affect engine revs nor any damage inside the casing, but the the engine cradle plate was distorted and needed to be forcibly bent back to straight before I could fit the proper spacer. Check if yours is now bent by placing a straight edge ruler on it.
 
At the beggining when in neutral the engine was able to rev up to 6000rpm but no more.
The fact is that due to the wrong gearbox to chassis installation the primary transmission chain was rubbing on the case and to my understanding this high friction was reducing power to the engine and probably not letting it rev.
In fact the friction increased the more I drived the bike and finally the engine was not able to idle and stopped. I tried to started up and there was a lot of friction using the kick starter pedal.

If you consider I should check out anything else I am ready to do it.
As a resume of the post I made the following to the bike:
ELECTRICS
-New Lucas individual coils with leads, caps and Champion N7Y spark plugs.
-New Boyer MKIV electronics Ignition
-New negative earth wiring with Motogadget M-unit electronic sistem
-New STATOR THREE PHASE (WASSELL) Alternador Lucas WW10192L 12V, 14,5 Amp High Output
-New SOLID STATE POWERBOX REPLACES RECTIFIER & ZENER DIODE, SUITABLE FOR 3 PHASE

ENGINE
-Refurbished head with new valve seals with new head gasket
-Refurbished barrels with new rings
-Revised and properly adjusted timing chain and camshaft sprocket
-PCV BREATHER CRANKCASE VACUUM NON RETURN VALVE
-Oil pressure gauge
-Refurbished oil pump
-New Triplex primary chain
-New STARTER SPRAG BEARING CLUTCH
-New HYDRAULIC TENSIONER PAD, PISTON AND SPRING
-New Barnett clutch plates KIT
-New AMAL PREMIER 932 Carburetors with 260 Main jet, 106 throttle jet, 3 1/2" throttle slide cutaway and 19 removable pilot jet.
-New K&N single open air filter without air filter box
-New open peashooter style silencers with new unbalanced pipes

-Rebuilt GEARBOX with new oil seals and KICKSTART SHAFT BUSH

The bike has been completely rebuilt from scratch including brakes, brake pumps, new disc brakes, refurbished wheels, fork with Lansdowne Dampers, new Ikon shocks.

The only part I have not done myself for it was already refurbished by the man that sold me the bike is the engine case with the camshaft but I properly adjusted the timing.
I see you have the micro digital boyer ei...but the plugs you listed are non suppressor type (no R in the name). Do the caps or ht leads have some suppression? I believe that boyer requires 5k Ohm resistance in the HT caps or the plugs ro prevent radio interfence of the timing.
 
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"Refurbished head with new valve seals with new head gasket" - seals and a gasket is not considered refurbishment of the head. Or did you do other things with the head?
Sorry for my poor english, I do not know exactly what refurbishing a head comprise but I mean mine has been restored with new valve seals, grinded valve seats and make the head perfectly flat again.
 
The other things that can be done are replacing the valve guides and replacing the seats. Very rarely do the seats need replaced. If you replace the guides you must have the valve seats recut with a proper valve seat cutting machine. If the guides are with in good tolerances you can usually get by with lapping the seats with some valve grinding compound and a lapping stick. You can check for good valve seal by installing the valves and springs and then by filling the combustion chambers with gasoline and checking for leaks into the inlet and exhaust tracks. Head bottom surface should be checked for warpage and milled the minimum amount to get flat.
 
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