Okay, so I've worked out all the other problems I had previously. Bike shifts great now and I can find all the gears.

The only problem I have now is, after shifting to second and giving it ANY acceleration, it pops into neutral. Every other gear is fine, second just won't let me speed up.

Also, it doesn't seem to be effected by RPMs, as I can downshift into second to slow down and it's fine, but as soon as I give it throttle it pops out.

Any ideas?

 

When the dogs on your gears wear out, they tend to kick out of engagement when under a load. Look at the pictures on this site. It's not a CBR, but the images are clear and you can see how the dogs stick out of the side of the gears. It helps them engage with the gear next to them.

http://www.goldwingfacts.com/1200stripdown.htm

 

the only problem i'm having with it actually being the dogs is that every gear worked perfect right before the motor was torn apart and put back together.
i'm really looking for potentially a misplaced (or missing) washer or something of that sort that would cause this problem.

 

OK, I see what you're talking about. But consider this. If a washer or spring is missing that holds or presses the gears in place, you're still talking about splitting the case again.