I'm pretty big on books. I'd start by confirming my commitment to a bike that doesn't run and is missing parts.
If I decided to commit, I'd procure the parts list, a bona fide manufacturer's shop manual, and something like a Chilton manual for the motorcycle. Depending on how mechanically inclined I was, and how much I knew about motorcycles, I might also obtain Honda's Common Service manual. (You can download all three in pdf format, from
http://www.honda4fun.com/home.php - under "Materiale". I think some of the guys have mentioned a few other sites where that info is also available. For the Honda bike specific shop manual, however, I'd try and buy an original copy from ebay or somewhere. You just can't beat the quality of those original photos.)
While I was collecting those things I'd start a "data dump". I would jot down every task I thought about, that came to mind, and just keep adding to the list. That clears my mind. Then I would start "chunking" together items from my data dump. I would probably do that on 3 x 5 index cards, and expect they would basically break down into cards headed with the bike's systems and subsystems. For example, the data dump might say "find a front brake that fits", 'rebuild master cylinder" - and a few additional related things. At a certain point I would label a card "front brake". I'd use pencil for everything but the headings on the cards, and the first thing on the "Front Brake" card might read "make a list of the parts I have that I can use". 2nd on the list might be "research 350 front brake rebuilding on web". 3rd might be "make a list of parts I need to restore front brake system - master cylinder, lines, caliper, rotor, etc.
Personally, I find that I often don't use this stuff after i write it down - writing it down in the first place is all it takes quite often, for me to progress quickly. Everyone's different, and you might legitimately think "there's no way Brown's way of doing things is even remotely how I would approach this project". That's cool too.....
But you did ask - and that's how I would start.
The only other thing I would try and do is "chunk" some low hanging fruit, to start. I mean don't try all the tough stuff all at once, with no easy, high return / quick gratification stuff thrown in. For me, an example of a "low hanging fruit" task was drilling out my brake rotor. It was easy, I loved the way it looked (looks), and just looking at it gave me motivation when I was stuck in the middle of something far more difficult and demanding.
Welcome and the best of luck to you. I know it's possible (and likely) you'll find a deep sense of accomplishment and satisfaction through your endeavors.
