It doesn't sound like you did anything wrong, it just sounds like your syncros are shot.
It's just probably becoming more pronounced because of the extra bite that new clutch is providing.
97 Aspire w/K03 turbocharged b6 SOHC
CoolingMist Varicool II Meth injection
Phantom gripped and cryo'ed 5 speed
^^Yes, it could be your synchros. But it most likely is your input shaft bearing is shot. My 5 speed did the same thing and it started with 4th gear. If you were to grab the input shaft while the tranny is out, I bet you are able to move it in and out over a quarter inch. You can get new bearings at Advance Auto Parts. However, if you need syncros, you will need to get an overhaul kit and they are harder to find for the 5 speed than a 4 speed, at least in my experience. I do have a local source (and the only source I can find that is reliable) and the kits are under $100. Let me know if you will need one once it is determined that you truly do. Also, you may be able to get another 5 speed relatively cheap from a j/y.
I forgot to add that when I took my 5 speed apart, the input shaft bearing fell apart.
01 Chevy Impala 9C1 police package "Unnamed yet". 154K
88 LX 5 speed "Silver PHOENIX" Currently being rebuilt inside and out. 400K
88 L 4 speed "Cherry Bomb" saved from the car crusher just in time. 186K
06 Ford F-150 Pickup Replacement for my 2001 Impala Cop Car that lunched its engine.
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