SquareSoft0 said:
One part of the problem is already fixed, the one that isn't fixed is this: My game freezes at the start of any battle.
Must be your settings or rom. You never mentioned if it's a GoodN64 verified good dump.
I only ran Pokemon Stadium 2 very briefly but watched the initial attacks from both parties for some random battle for the impatient.

Damn what a weird game.
I noticed no auto-controll or anything and I'm still using 1.4! (Jabo 1.40 audio + video and NRage for input).
Make sure you use DEFAULT settings! That is disable everything in the adavaned tab of graphics if you use Jabo's Direct3D.
I noticed you mentioned "Direct 3D T&L HAL". This is a very bad idea. Stick to the non T&L one.
Btw. at the beginning of using PJ64 I wished there was a button "reset to defaults".