I'm on the second rebuild of an AT right now. Engine is about to come out, and get split open. I rebuilt the first one and rode it down the coast of Africa, leaving it in a crate in Mauritania ready for the next leg next year. Had so much fun rebuilding it, thought I'd do another - same year (2002) same model (RD07a). It's not that difficult a job. Just bag and tag each group of bolts, etc as you go. Follow the Haynes manual assiduously, and compare to the Honda Manual often. Have a chat with Jonathan on this forum, and he can help you with parts and has a good little pdf that helps breakout the parts which can help enormously. Make absolutely sure you undo the Clutch nut while the engine is in the bike and still attached to the chain - believe me when I say it is soooo much easier to do on the bike than off!
When you put everything back together on the engine, you should replace all bearings (including ones folk say don't bother with in my opinion), check big and little ends (although it's rare to see much wear on them), replace the piston rings (obviously check to see if you need a rebore, but likely you will just need new rings if you are blowing any smoke). If you are going all the way down (recommended), then replace the output shaft if there is any wear at all on it.
As you build it back up, make sure you use a torque wrench - you will need a little one for low torque values and a bigger one for the high torque values. Buy a cheap micrometer while you are at it to check everything else. Also check valve stems, and replace as needed (not hard), and obviously check for any valve wear. Check and replace cam chain tensioners if you need to (again, fairly rare from what I have seen), and double check all your gears are ok.
Personally, I use a small dab of loctite on every single bolt as it goes in. use a loctite that is meant for the environment it is going into - I don't remember the number I used offhand, but the one I chose could handle high heat ranges.
Then after the engine is all back together, crank it over slowly, making sure TDC on the timing chain is accurate, everything turns smoothly in neutral, then gradually work through the gears up ad back down. If everything is good and smooth, then put it back in, again loctiting bolts as you go. getting the engine in is a bugger - make sure you put it in sideways, then it is a case of tilt, lift and turn slowly - it WILL go, you just need to get it perfectly in position.
While the engine is out, clean and inspect the frame, get rid of rust, check welds and powder coat if you want to go that far, or simply use etch and spray to touch up.
That's the big items I learned on the last one I think. It's done 4000km now and was going strong right up until it was crated. Drop a line if you get really stuck, or aren't sure of a step, and I'd be happy to offer what advice I can - note I am not a mechanic, just an engineer...!
Oh, and I replaced the water pump with a facet, and the reg/rec with a mosfet - both are a peice of cake, as long as you do it properly with solder and heatshrink for a really nice water-tight finish.
Cheers,
James
