I'm afraid I can't help you with the clutch issue either. You might want to start a separate topic on that (in the appropriate section, or risk the wrath of Hondo, God of NHF

).
Good suggestions on checking the oil level; I don't have much to add other than this: If you're going to lean down to check the oil while you're on the bike, for god's sake make sure your kickstand is down in the event you lose your balance. My 550 has a centerstand and it's the only bike I've ever owned. I don't know that I would get one without a centerstand now. It makes life SOOOOO much easier.
You can get the replacement Operator's Manual through Honda direct, through the link posted above or possibly on ebay. But you'll also want a good repair/maintenance manual. The actual Honda shop technical guide will probably be kind of spendy, but you can get them on
http://www.repairmanual.com/. They tend to be a little better than the third-party products, but sometimes it'll specify special tools or assume you have more knowledge than you do. For most stuff, a Clymer's manual will serve you just fine. I have both for my 550, and I rarely find differences between the 2.
Welcome onboard.