Have you checked your tq arm bolts? Known to loosen up sometimes,and since you jsut did the install, maybe did not tighten them? Driveshaft problem possibly. And yes, it could be a problem inside teh tranny, but kind of weird that your tranny shifted fine BEFORE the gear install, and now it shifts bad AFTER
I would think it would be more rear end/driveshaft/tq arm.
Is your tranny due for a service? If so, go ahead and drain teh fluid to check for contaminents. If not, I would start out back...tq arm driveshaft rear end.
Once you make sure tqarm is bolted up and tightened correctly, maybe you can borrow another driveshaft from someone? Also, did you check pinion depth when you did teh gears? Or did you jsut check backlash on ring gear during install? Did you reuse the shim from teh 3.73 pinion on teh 4.11 pinion? What pinion spacer did you use? Steel or crush?