The top three pop bumpers don't light until you clear the left drop targets (I think). The two side ones don't light until you clear another drop target bank (twice maybe, can't remember). So them not being lit when you start a game is normal. Experiment with the glass off and you'll figure out when they light up.
The 2.5A SB fuse usually blows when a special solenoid locks on such as a pop bumper or slingshot. The pops (except for the lower right one) and slingshots will all fire and stay locked on if one of their switches is stuck closed, which blows the fuse. This is common.
Other reasons for the fuse blowing is the game having issues due to the 40 pin connector aging and losing reliable contact between the MPU and driver board. Another reason is aged or bad sockets on the MPU (Scanbee type) that can cause game lock ups and locked on coils.
Special coils can also lock on if the resistor or capacitor on the switch are faulty. I've seen pop bumpers lock on intermittently and blow the fuse due to the capacitor being bad.
No reason to go back to the System 4 board unless you are having problems with the one currently in the game. Both boards will work fine in the game.