Wellll,, lets see,, nope - I have never done a KTM top end.. GUess I am not gonna be much help to you.. Maybe some off the cuff stuff would help:
I like to leave the engine in the frame. That way it isnt roling aroundwhile I am trying to work on it!!
Take the tank, seat, platic all off and hit that baby with the power washer,, Payclose attensioni tothe areas abaove the jug - claen now pays BIG later!!
I like pulling the jug with the head intact - it protrects the engine alot, right after removal you should cover the rid and open case area with rags,, That open bottomend is volnerable in this position,, WOrk above the cranck case with a good rag block stopp stuff, Remove the pistoin from rod using a puller - NEVER try to drive it out with a hammer. THis is very tempting but puts alot of pressure on bearings on the big end, Piston off, remove the smal end bearing abd clips while keeping the case coved real well, CLean ALL surfaces clean of any left over gasget material, Heres a hint, even if you didnt damage the old gasget can you reuse it and save some cash/// THe answer is no - put in knew.. Examine the port area in your just for chips in the Niclsil, Look carefully becasuse a simple little nick now is tommorros MAJOR MOTOR JOB!!! Look for aluminum smeared on wall of jug, if you have spots the way to clean them is with Muratic Acid - NOT WITH A HONE STONE!! Put acide on a q-tip and carefully work the spot - dont go beyond the original coating becsue thus stuff dont care what aluminmu it eats!!
Using a dial bore to check the taper of your jujg is a good idea!! THere is a good selection of good pistons out there.. THere is a new on the line that has Tephlon covering the lowerhalf.. Last I heard they are AWESOME!!! I beliefe they are aftermarket Japenese and qujite reasonalble tto.. Watch the ring gap on what ever you use, Also - Cometic Gaskets have givin us fits on fits,,, Vesrha fits much better,,, Of course, OEM works great too!