Hard to advise you on what is wrong without knowing what has already been upgraded or replaced on the bike over the years.
And by "wrong" I mean the bike is not running or braking properly (you refer to "if" it smoked on startup, which i take to mean that it actually does smoke on startup ??
But, if this helps, here is what I did to my Mark III when I bought it 4 years ago, with 14,000 miles on it and having been sitting most of the previous 15 years:
Repaired or Replaced right away:
- front and rear brake master cylinder rebuild - both were leaking so rubbers had to be replaced
- ditto for front and rear brake calipers - one was stuck, the other suspicious
- valve seals - bike would smoke on one cylinder after it got hot enough (about 10 minutes of riding)
- fork seals (leaking)
- tires (both were old and brittle)
- various fasteners that had rusted (with stainless)
- clutch plates (with Barnett plates). Old ones had become "varnished"
Upgrades which soon followed:
- Sparx 3 phase alternator and regulator/rectifier
- single 34 M Mikuni carb (bolt on and forget, in my experience), and accompanying K&N filter
- resleeved front brake master cylinder (big improvement - should have done it before I rear-ended that car!)
- heavy duty starter cables
- PCV valve on the breather line to the oil tank
What I delayed and should have done immediately:
- transmission lay shaft bushing (it died on me while riding, locking up the rear wheel, and luckily I was going 5 miles an hr in a parking lot)
I'm sure the smarter folks on this forum can suggest other things too.