Well, sooner or later you're going to have to get those plugs out, so you might as well get on them. Hit them with PB Blaster or another penetrating oil (although PB is the best), and wait a day or two. Then when the engine is cold, wrench them out. Never heard of someone stripping threads getting the plugs OUT, unless they were super overtorqued going in. Usually people strip threads overtightening the plugs when they put them in.
Sounds like you're running rich: if you remove the air filter, more air gets through, leaning out the mixture. Do you hit this 7000RPM "wall" at 1/4 throttle? 1/2? 3/4? WOT? This will tell you where the problem in your jetting is. If you hit the wall at WOT, your main jet is too large. If you hit the wall at 1/4-3/4, your needle clip is too high. Doing a "plug chop" (search the archives for loads of threads about this) will give you a more definite answer. On the other hand, if it was running like a dream when you put it away, I'd look at cleaning the carbs, especially the float levels.
First thing though, give the bike a tune-up: plugs, adjust cam chain, adjust valve lash, adjust timing. Then give your mixture problems a look.