Amiga 4000T Mouse Troubles

[amiman99]

So, why you tried to install something on a live system? You're asking for trouble.
Anyway, as a workaround, you could use temporarily a serial mouse until you fix what ever you broke. You'll need a driver in a WB Startup folder and a 9-25 pin converter for your serial port.
I did that on my A3000 when I lost my mouse do to someone damaging one of the ICs.
Looks like mouse movements are controlled by PAULA, maybe you can replace that and see if it works.

[amiman99]

Castellen was right about the movement, pins 1-4 go to the 74hc166, which you said that joysticks movements are working. Have you tried to play a game?
The Buttons 2 and 3 on the mouse go to PAULA on both ports.
Button 1 on joy/mouse go to CIA U550

Maybe your mouse is not working, did you try another one?