Drop the engine it'll make life so much easier!
When you pull the heads you are going to loose the compression of the base gasket, which is an area that has had problems on these bikes. You're going to want to inspect the base anyway to see if the cylinder assembly has been hammering it. See here
(or goggle Pyndon base gasket)
Q: Why would you want to raise the compression further than it's already-high 11.5:1? Assuming it's a street bike you're going to have to run the best gas you can find (I hear 20% ethanol is the new goal in the USA). How are you going to accomplish this?
The ports on these heads are atrocious- Marc Salvisberg of Factory Pro/Wheelsmith Racing
talked about seeing up to 15hp on his dynos from cleaning up the ports! Casting remnants & irregularities with machining that KTM seemed to make no effort to blend surrounding surfaces! This is something other companies (including the Japanese "Big Four" with their higher production rates) have been paying attention to for years now. Polish the exhaust to a mirror finish, while the intake should have some
texture in it to keep the fuel atomized in the air stream... smooth the ends of the valve guides in the direction of flow but don't
remove any length from them so they can support the valves as much as possible.
Since you've got it down this far measure your valve springs for height & compression, and remember to send your intake manifold rubber boots so they can be matched with the intake ports/throttle bodies.
You're gonna love it when it gets back together!