Started the bike the other day and heard this weird sound, put in gear and road home. Got home, put it in neutral and heard in again. Turned it off, then on and the starter was cranking. Oh s__t. Started for a couple days and now just a whine when I hit the start switch. Any thoughts on what I fried?

 

Starter solenoid at a guess. Right side of the bike, next to the main fuse (30A) - probably green.
http://cgi.ebay.co.uk/Honda-CBR1000F...torcycle_Parts
Or maybe the starter clutch - I have a good spare if you need one......

 

I sounds like the starter was sticking on. Two things can cause this, the starter button itself (or short in wire) or the starter solenoid as mentioned. The switch and wire are easy to check. The solenoid is an electromagnet with a plate that shorts the battery terminals that are hooked to the top of the solenoid, when the button is pressed. If the plate is stuck in the short position, you will see continuity across the terminals with the key off. The best way to check that is to see if you have 12 volts from the far side to ground. Sometimes you can free the plate by banging on the top of the solenoid with the butt end of a screwdriver.

If the bike was running with the starter stuck on, the starter clutch would be over worked and wear out. It sounds like you have both conditions. The stuck starter trashed the starter clutch.

 

Thank you very much guys. It gets better, I decided to take a ride this afternoon, so I pop started it and took a ride, it was running very poorly under 2000rpm. then stalled on me. Got it started again and was running poorly so that I had to keep it at 4000 to keep it running. Then it stalled on me again. It seems I have some spiders in my electrical system! Maybe that reg/rect I bought a couple years ago might be needed after all. Thats just a guess, Mr. mechanic, here I come!

 

Check your battery........................only gives the battery enough charge above 3000RPM.
Read the posts on starter damper too.............
Reg/rec could be cooked..................the originals were never much good.