You'll have to do your own price shopping.
As for your chain preference, I haven't a clue. The stock chain is a DID 428 and it is junk. Be sure that isn't what you are getting. If you want a Lyle Racing DID 428 chain you'll have to contact Lyle Racing for their price. Other places sell the same chain for different prices. If you want really cheap you can probably find a set of sprockets with a cheap chain on ebay for under $50. Yup, took all of 30 seconds to find the stock sizes sprockets with a chain.
Stock sprockets in North America are 14 and 50. The Yamaha sprockets are good quality, as are JT and Parts Unlimited. You'll have to do your own shopping. Really, is it that hard to google?
Side cover gaskets? www.stadiumyamaha.com Order along with sprockets. $38.10 for all three parts, plus shipping. They've never charged me more than actual UPS fees.
I have no idea the specific sizes of the side cover screws for either side. Pull the screws and take them in to match up. Try to find stainless allen heads to fit. Less likely to round out next time you need to remove the side cover. Maybe there is a kit available? That would be convenient, and probably cost less than buying screws individually. Google is your friend.
Ebay to the rescue--took 30 seconds to find these with the ebay search engine.
Rear tire options in North America are limited to Bridgestone TW34 (stock) and TW204, and Shinko clones of the TW204. Front tire options are limitless--there are several front tire threads. There are several replacements for the front tire that work much better on and off road. As for prices, google. I like www.americanmototire.com They have the TW34 for under $100, which is pretty cheap. They also have several good, cheap options for the front. First is the Shinko 700 for about $65. They have the Kenda 270 for about the same price and Shinko 244 for about $10 less. These two are in 5.10-18 size. All three are better than stock, which they also have for about $70. They also have the Cheng Shin clone of the TW31 for about $60, but it is no better than the stock tire. Free delivery on whichever you choose, too. Free delivery is good, no?
Anywho, some times the cheapest advertised prices aren't cheapest delivered prices. Shipping and taxes can make or break a deal. Be sure you compare delivered prices. Tired of being told to google? Prices at various sources change on almost a daily basis. You'll need to do your own research in real time to find out where the best prices are right now. Ebay's search function works well, too.