I'm installing my empeg in my 99 wrangler sometime in the next couple of days, but I'm not going to put it in the dash.
Im going to install it in my Tuffy stereo console. I know the angle might be bad, its not as secure as I think, blah blah blah. Im gonna do it anyway.
The amp is going under the rear seat, and I was going to leave the stock head unit in place.

Now my question is can I just tap into the stock head unit, while leaving it and its wiring in place, or is that a bad idea?
I was just going to run new wiring from the stock HU to the empeg, and new wiring from the stock speakers to the amp.
I want to leave the stock head unit in place, as a distraction to would be thieves and for the clock. Ive got a tuner so I dont need it for the radio.
I also just dont like the way the empeg looks installed in a non DIN slot.
Tuffy's already purchased, so thats where its going, its just a matter of whats the best way of wiring it.
Anybody have any opinions on this method?

Too bad I didn't know... I could have sold you my Tuffy stereo console since I don't use it anymore. :-) I bought it when I bought my empeg so I could mount a cdplayer in there since I didn't think I would enjoy not having a cd player. I was wrong about that one! Never used the cd player again.

Anyway, I did it exactly opposite of you. I installed the empeg in the main stereo slot hooked up to the factory wiring, then hooked the output of the tuner/cd player in as "Aux" input to the empeg. I used the factory wiring for my speakers and ran them to the two amps I have under my rear seat. I also just spliced the power from the tuffy head unit into the factory wiring for the Jeep and it worked fine. I believe I also got a higher rated fuse as well since I was powering two units instead of just one.

A problem you might run into is heating. The empeg runs warm, and has vents on the top to facilitate airflow. Since the Tuffy is vertical and doesn't have much room on either side to 'breathe' (and it is steel with no ventilation) you might want to drill some holes in the proper side to let some air in.

Just some things to think about.

empeg + Jeep = rox!

I did a similar install in my VW (oh and in your's as well ;-)
I would just leave the stock speaker wiring in place and splice in the new wires from the amp. No need to run 4 pair from the seat forward, just tap into the rear sets at the rear, and then run 2 pair to the head unit and tap into the existing front set.

That way both are live and if you don;t have your head unit you can listen to the factory one, (although I wouldn't recommend running both at the same time) if you were really paranoid you could get the auto switcher from Sony, but if you don't really care then just you be carefull, You could always install a kill switch for the factory unit under the dash so there would be no "accidental" mishaps.

As far as the angle is concerned, disk is cheap, just make both empeg's a clone of each other, and when the HD in the one in the jeep dies buy a new one and swap it out.

Not sure about the venting issue, I think that holes in the Tuffy would defeat its water resistance capabilities. Probably best to leave it home when you go the beach on a hot day.

Peace!

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I will be at the New york meet with my 97 TJ , tricked out.