what's odd is that initially the ball would kick out and you could play the game without the pop bumper working, indicating F4 was still fine, so it sounds like the transistor failed by going open.

Now after replacing the transistor the fuse blows.

Just to check, are you sure the orientation of the transistor is correct?
What transistor did you replace it with?

With the game off, if you put one lead of you multimeter (set on continuity) on the metal tab of the transistor and the other lead to ground, do you hear a beep/tone/zero resistance?

There is a chance the diode is shorted on the pop bumper, you should check this.

For the fuse to blow straight away there is a short to ground.

Sounds like bridge 2 may have shorted internally on your lower power board, but you say the game boots with J5 removed so it won't be this.