I don't like the jackshaft idea.
Aye Lucas...a sticky wicket there... I'd have done it first if an engine had fallen in my lap... sleep on this... the pieces you have might fit another engine. I rode a friends DR650 again the other day.... very acceptable vibration, a starter that always works and, after seven years renting and doing tours through Central America with them...reliable. Air/oil cooled and torque enough. I'll offer Fast Eddie Moran a drinkipoo and break out the tape measure tomorrow.
The tank should be adjustable with heat...no? No need for heroics there. Exhaust you can do...well, just repeating things here. If you fixed everything, at great cost in agita, you'd still end up with the very important countershaft sprocket height. If it's cold where you are, I have a small shop here in Costa Rica and a machine/weld shop next door.... I have a couple LC4s....