Randy,
Hey there. I thought I'd throw in my .03 cents for your concerns.
As far as inspecting your hubs, I wouldn't worry too much about those unless your rear sprocket has come loose before. Just make a quick look at it when taking off the rear sprocket for replacement.
Now, as far as gearing, the stock gearing I believe is 14-49, but don't quote me on that. I know my brother is going with a 14-50, so up one in the rear for a little more
torque off the bottom. Who really needs to go 90mph on a motocross track? I would definitely change the rear sprocket bolts and nuts as a precautionary measure though. Also, use a locktite substance on them when assembling. Torque them to the required spec's, don't overtighten, as the locktite is designed to keep them in place. I think some guys were using red locktite. I'd ask others about this though. Red loctite is very hard to get loose once you use it. So, maybe blue would be better.
As far as your chain, I went with an O-Ring 520 DID chain. I think it's 114 links, but the shop will know when you tell them what bike it's for. The master links are kind a pain to get on since the have to be pressed together. Be sure to use the O-Rings they give you for the master link. Also, make sure your chain is properly tensioned. I use the three finger rule too, but if you have to measure, then measure. Check the manual on correct adjustment. The O-Ring won't stretch like the stocker and it will make your sprockets last longer. Just be aware, when pressure washing, be careful not to blast the chain since the O-Rings can be hurt by that kind of pressure. Just throw some WD40 on it after you wash the bike and she'll be ready to ride for your next outing.
Swingarm: Take the rear linkage apart and pull the swingarm off of the bike. Be carefully since there are loose needle bearings in most of these, so all you really need to do is wipe out the stuff if it still looks clean and apply some Bel Ray waterproof grease to all of your pivots. You shouldn't have to replace any of those bearings. Just lube them and reassemble.
Do the same for the headset. This is a little tougher, but just have someone help you, since the forks and bottom triple clamp will want to fall away from the bike when your getting to the bottom bearings. Reassemble and remember to leave the headset a tiny bit loose when tighting the top triple clamp bolt, since this will tighten it up a little once torqued. Then be sure you properly torque your top triple clamp bolts around your forks to 17 ft. lbs..
Ummm.....
Clutch: Replace that clutch hub with a Hinson. This take a little mechanical know how since you have to remove the gear off of the stock hub. Your Hinson will come with directions, but you may want to have a shop grind off the rivets for you. You'll either need a grinder or a large drill bit to get the rivets off. I've also heard of guys drilling from the inside of the basket since you know your not going to reuse the thing, just drill the heads of the rivets off so you can get the rear gear and springs off it to put on the Hinson. Use red locktite again on the three Hinson bolts to assemble the gear and spring plate to the new basket.
I would definitely stick with stock Yamaha OEM clutch plates. Just replace the fibers, you should be able to reuse your steel plates that you currently have. Other's can comment on this if they'd like. When I replaced my Hinson, I only had one ride on my bike, so my fiber and steel plates didn't have any real wear on them. If your clutch is making all kinds of noise right now, I may just say replace all of the fibers and the steels to be safe. It will work great once you have the Hinson in there.
I wouldn't worry about your gas tank unless you visibly see gas leaking or you can smell it over the smell of your three week old jersey.
You could replace the fork oil with some good Golden Specto stuff. Not sure what they use as the stock fork oil weight though. Check the manual on that and on how the fork oil levels should read.
Other than that Randy, I wouldn't worry about much else. The stock air filters are fine and I bought a Uni Filter to have just so I don't have to wait for one to dry to put a new filter in. Do make sure to put grease on the lip though when putting a fresh filter back in, along with the proper amount of filter oil of course.
Let me know if you have any other Q's. I'm happy to help. My info may be a little off and all you other guys can correct me if you'd like. I'm not perfect, never claimed to be.
Daveyg