There is a lot going on when you changed pick ups. EMG's have the pre amp built into the pick up there for needing a battery. Did you wire the other pick ups to the EMG pots? If so did you disconnect the battery? The pots That are used for EMG are 25k And the pots for passive pick ups are around 250k to 500k. I don't know if the combination would work (Passive pick ups with 25k pots and a battery).
The first thing I would do is replace the battery. Check the amp,too. Plug the chord into the amp and turn the amp up a little bit and touch the tip of the chord at the other end. If you hear a pop, click or buzz the amp should be ok. I had a battery short out to the amp and fried the volume pot in the amp.
Double check your wiring and make sure it is right and no strands are touching other areas.
Tedward