2002 T5 transmission vibration issue

I installed a new Ram clutch and flywheel. The shop before left the transmission and flywheel unbolted by about 1/2 inch (roughly, the bolts have red Loctite, so within 47k miles, I don't think it backed out that much). I finished and drove around, and there's a rough shake at idle, and around 4,500 RPMs, it gets violent enough that you have to let off because the car shakes and the shifter bounces, enough to force itself into neutural by just pressing the clutch pedal. I double-checked all parts and they are correct for my vehicle. I'll have to pull the transmission out in a couple of days to put a new bearing retainer in since it's pitted, so I'll recheck the clutch assembly again when I do. But I'm thinking my input shaft and internal bearings got destroyed. Doing a flush, the mix of ATF/gear oil they put in had a metallic shine. If anyone has any other thoughts or help confirming what it could be and what to check, that would be greatly appreciated before I throw money into a rebuild kit. The mounts are still usable, and the flywheel is internally balanced.
 

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