Obviously I would give you some advice about gearbox assembly if I knew. Sorry, no such wisdon to impart to you but I do have a bit of experience with an aftermarket quickshifter. The one I use on my ZX-14 (HM Plus) doesn't work very well at high rpm unless you use a very slow kill time. It has produced behavior with upshifts EXACTLY as you have described. ---clutchless shift up, does not engage the next gear, engine spins like in Neutral. The gear position arm does not have enough kill time to climb over the lobe on the shift cam (star) and it apparently hangs up on the lobe putting the transmission in NO gear. After a few hangups like that, a missed shift now results in the transmission slamming back to the previous gear. Needless to say, I'm hesitant to use the quickshifter under hard load until I can figure out some way to preset proper kill times for gear and rpm.
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Let me ask, have you had similar experience with your quickshifter? After missing a gear and a second or two passes, it can be very difficult to judge the proper rpm to blip to execute a smooth downshift. I slammed my gearbox a few times after a missed shift. I got metal slivers like I see in your photo. They came out in the oil change and magnetic oil drain plug. For now, I don't dare use my quickshifter over 8k rpm.
What I'm saying is that this could be a simple case of doing a terrible downshift at high rpm. That might have broken something.
Sorry. I wish I had a lot more knowledge of gearboxes. I might be able to tell you what broke and we would have a better idea if the quickshifter/bad downshift theory is correct. Seems possible especially if you experienced clutchless shift problems before the rebuild.