You have blown out the audio section of your IJ that you were running to the subwoofer. The speaker driver will be fine, the little amplifier will be fine, but your board is screwed. As others have mentioned, the cable you bought DOES NOT convert the signal from high level to low level.

What you did was run a high level signal meant for a speaker with a 4 ohm load into an electronic device without the same resistance. It can't handle that, and now it is toast.

The signal being "crossed over" or not has no bearing on this. The only way to remedy this is to repair or replace the board in your IJ.

I am really sorry that this happened to you. I hope that it is an easy fix too.

Here is what you should buy:

http://www.parts-express.com/pe/showdetl.cfm?partnumber=300-782

The amplifier has high levels inputs designed exactly for your situation. It has an adjustable crossover to dial in the sub. It also has a gain knob so you can match the levels with your main speakers. 25 watts is PLENTY of power for a small sub driver in a large open cabinet like a pinball machine.

This will do everything you are looking for. Get this, mount it in your cab and you will be good to go! I've probably used these half a dozen times for various audio systems. It will take the guesswork out of your setup.