Thank you all for the replies. I have been working on the bike over the weekend and found out the following:
1) The engine clunking could be the decompression issue as I had the local KTM guy look it over and he said that the starter clutch going bad would happen more frequently if the bike was hot and usually ends up with the starter spinning and/or burning out. We tried a few times starting the bike when I got there and (of course) it made no sound at all when started multiple times. Anyways, I'll keep my eye on it just in case, and am ordering the SKF 19993 Seal as a backup when/if the starter goes.
2) The brake light problem was traced to the front Magura brake switch. It kept going through bulbs because the switch was constantly on, burning up both filaments at the same time as well as one of the bulb contacts. Some CRC-556 (WD-40 for you folks) and some dielectric grease on the contacts helped it out. Now I need to find a suitable LED replacement, although I am hoping the vibration won't bring about an early death to it as well.
3) Stalling seems to be better, have messed around with the idle a little and also ran some seafoam through the engine, seems to idle smoother now as well. I will be doing the spring/drill slide mod in the near future as well as rejetting for both the KTM race muffler and side airbox. I thought I might as well do it all at once instead of constantly rejetting/setting up the carb for every little mod.
Thanks again to everyone that replied, hopefully I can get it all set up perfect and keep having a blast on my first supermoto.