built a rack for the amps for the jeep, stacked them with room for them to cool.
cut out the kick panels for front speakers.

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link to my pages (http://cetrov.com/stereoinstall/tj_stereo_install.htm)

so where does the subwoofer go?

I have a box built for the subs- removable- also the stereo has seperate lines out for subs- so for really thumping sounds I just plug in the subs to the second amp, drop in the box and let it rock. If I need the space or will be somewhere I don't want to leave the stereo out in the open, I just remove the box- leave the stereo without the subs and it sound fine. the speakers are all installed into the body of the jeep and the sound bar- so you don't see anything that would be worth taking.
The dash mounted speakers will have to be eliminated I think, when the roll cage is done- the bars are going behind the dash down through the floor.
I need to find some flat ducts to redo the vent system for the two end vents as the roll bars will have to go there too. I don't want to lose the heat coming from those vents as the left one blows hot air on my hand on a cold morning.

Still working on some places to install tweeters and more speakers. I have some mounted into the half doors but loose them when the doors are off. I just added a plug to the wiring so when you remove the doors you just unplug the speaker connections.