Quoted from homebrood:I had this problem too before and the remote battery makers need to have more thorough intructions cause it can cause fire and ruin games if not installed properly/ That being said...you're doing it wrong!
I would not necessarily say someone selling a battery holder needs better instructions (my pinballs did not come with instructions on where to put them, but I would guess not across a circuit board - just a silly example); more like anybody attempting to do electronic work and modifications needs to understand what they are doing before attempting. Otherwise, even a small job should be done by someone who is qualified.
@OP Yes, your wires originally "burned up" because all you did was wire 2 wires backwards and basically just created a short across your new battery holder. The blocking diode tried all it could to hold back the battery current; causing diode to get hot enough to melt things down. The holder you should have puechased for your game should have been one without the diode in the first place...
Luckily nothing got damaged during a mod to help prevent potential future damage.
Glad you got it figured out and that it is all working.