I went to do the valve clearance the other day, and couldn't get the EX and IN hashes on the cams to line up where they are supposed to be when the ignition pulse generator rotor is lined up, so I figured, "Hey, this is why the bikes been running like ****, I'll just straighten it out and she'll be purring in no time" Not quite the way it worked out, the bike didn't fire at all and had pressure at the vacuum port on the number one cylinder, so I figured maybe it was 180* out. So I pulled the cams again, rotated the motor over and lined the cams back up, and still nothing. Is it possible for the pulse rotor to be installled backwars? Instead of being marked with a Tl:lF like its supposed to, I see what may be KHB or R, the bottom half of the letters are obscured by the washer. Or maybe this is an aftermarket rotor. If somebody knows a good way to set the timing, besides the book way, help me out please, I'm out of ideas.

 

or just help me to be sure I've got it TDC

 

Firstly, you're only going to have one cylinder at TDC at a time, so I don't know how to answer your follow up post. As for the timing issue, I really can't say because I haven't done it before. I've adjusted valves on other bikes, but not my honda yet. I will say that the fact that the cams didn't line up with the IN and the EX was probably because they only line up every 2nd rotation of the engine, or maybe its only the 4th time around, I can't remember and I'm not sure. But yeah, thats probably where you should have stopped and asked questions. If the bike actually ran then they were probably in the right spot because if the cams were off by even a little bit the engine at the very least wouldn't run and at the most would promptly explode.
So right now my advice to you is to stop getting in over your head. Get the cams back the way they were before you took anything apart if you can, if not find someone who can. Don't pull off anything with the signal generator because that might be the only indicator you have of where the engine is in its rotation. If you screw up with the cam positioning then there is a good chance that you'll send one of the valves right into a piston and reduce things to a pile of junk.
Good luck