Well the KDX motor is more than just what you think different.
The flywheel is not that much different in weight, it is the extra drag from the lighting coil.
Stock you get thicker head gaskets on the KDX, the WR gears, different water routing thus different heads, lighting coil, different carb setup and pipe.
Really if you install the KX .26 headgasket, a good pipe, freshen the reeds (the VforceII is the best way) and jet the carb up leaner with a 1367 needle, 38/40 pilot, #6 slide, 155-160 main you will have a 88-91 KX power with the WR gears and lighting.
now chassis and suspension is another story.
For the cylinder repair, talk to Eric Gorr. You can sleeve the unit and run a 265 kit in there. Also get the cylinder ported out while it is there.