I think Morley ^^^ has a great idea of starting it with clutch cover off and clutch basket removed, you should be able to pinpoint any noise.

I'm full of great ideas that don't work haha.

Hey Morley you helped me when I was stuck.

Well, I pulled the crank seal and I found the problem. The crank bearing is definitely damaged. I don't know if I did it when I installed the crank seal, or if it was done during assembly. I don't know exactly what they are called, but one of the carriers that holds one of the balls in place in the bearing is broken. I guess I'm going to be splitting the case again :( I'm trying to attach pictures, but I guess pictures aren't working again.

The "cage". Sorry to hear that, but you're going to be a pro at splitting cases :o)

Live and learn, we all make mistakes.

Great job on finding the issue, I hate it when I know there is a problem and you take everything apart and all looks normal with nothing obvious being the problem and you are left scratching your head. At least in your case you found the problem and it was fairly obvious once you investigated a little further, now you’re scratching your head and wondering did you damage it on installation or was it a defective part from the beginning?

Oh no!  

Did the bearing have a plastic cage?  

No, it's a Koyo bearing with a steel cage.

Blimey, at least you found it. Try posting a pic link from some hosting site--Please. I used google photos recently & worked good but imgur seems the popular one although i couldn't work it out, wanted phone number if running it from a pc & wouldn't accept my number.

I used to use high speed bearings with a plastic "fiber" cage in my 100/125 race motor with no issues. Be unusual for steel cage to break when new or near new.