Smoothness is Commandoness, period end of story throw in the ole towel wrap it up, otherwise not a real Commando, just another vibrator ordinary cycle.
Greg, me steve is learning along with ya. I just dealt with too tight a fit of front iso in frame to even get it in with wedges beat hard to spread. I found the front tabs were a few 1000ths wider at bottom than top. I put in all thread rod to spread hard against the top of tabs while beating in careful with drift on bottom/rear of tabs. This gained a bit more parallel fit but not perfect. In the end I had to have machined off in 2 separate trial/errors .03" off RH of front mount for .06" total and then still needed wedges to ease in with wood block and easy sledge hammering.
Trixie was initially found with front tabs spread apart ~,09" beyond manuals spacing, sheeze. She is spread apart up there a bit more yet, but should work a treat. This Combat went silent about 2200 prior with adjustable iso's set nearly as close as manual lists. Her head steady was in great bind - under tube skewed over ~3/8", even with rubber 1/4" spacers on opposite mount sides. Only vibe detectable over 2200 was a buzz sense on intervals of strong side way head winds
or holding some turns that moved top of engine to compress steady to transmit.
Trixie is non-rodded, I rode her twice into hinged handling early on to know what to never-ever do again, so just sane ordinary turns I'm taking above.
As to the stem leaning, as you say its robust fixed to the spine so guess what gave in and should give again to bring er mostly upright, the down tubes. You don't know yet if that's even an issue, likely not. Trixie's T-bone deer strike bent forks easy visible and slammed apart my L knee on cylinder to bend the under spine tube, but the steering stem stayed aligned fine and so did the yokes. She rode hands off as good as any non tri linked Commando, slow to over the ton afterwards - but having to assemble with helper and terrific brute force. This time around I'm fixing her enough a single dumb mechanic can assemble with ordinary size tools and force.
I did decide to try what worked a treat in Ms Peel, I ground a 45' bevel on the front big doughnuts to narrow rim ~1/2 width, Hope is sooner stillness and no intervals of buzz from horizontal vibrations in side ways binds.
To tie frame down hard upright I'd use 2x4's across the tubes screwed/bolted at ends. But hey after I had Peel rear loop pinned and welded back on it still was droopy, so only way to move it was lifting frame over head and coming down harder and harder on carpet on cement. Not exactly a good example to follow I guess.
I've cut / drilled through various spots in frame and its un-settling to see how thin wall it is. Commandos are thoroughbred design is so many ways but the isolastic chassis/power unit tops the list to me.