Did you change the teeth on the sprockets? If so what to?
Also: I took my fairings off for the first time yesterday (at about 4am). It wasn't that bad, you just need to make sure you organize everything. Like label the holes, label the bolts, label every single bit (string helps, so you dont mark anything. just write on a piece of paper (numbers work, so do letters, or any other specific code you want) and tie the string through any holes, around any pieces, etc. and to said marked paper. for example: you'd label every hole A that fits every screw A, etc) That way you know exactly how to put it back together.
Also it would help to keep a journal/note of everything you do, and in what order. so when you go to do it again, you know how to (or if you forget how to put it back together, usually just reverse the order)
I'm not sure if it's been posted, but gstwin.com is a really REALLY useful site for gs500's. You don't even need to register (unless you want to ask questions. but most things have been asked/done so the search function will most likely be your main friend). Personally, I haven't registered on the site, but always visit it and search/browse (because every question I've had has been answered already)
As cbcanada said, ''just do it''. If you have the time, tools and patience. It really isn't hard, and if you mess up-- well, that's what friends are for! (payments of booze seems to motivate people pretty quick!)