1. Where did you put the amp so it was out of the way (...) I thought about buying a TUFFY security drawer for under the rear seat

This is not empeg-specific. See this FAQ entry. However there are a couple of Jeep owners on this BBS, maybe they'll jump in and answer here?

Where did you find the flace plate to adapt the chrysler 1.5 DIN to the standard 1DIN sized dash opening?

These are absolutely everywhere. They are very common, any car stereo installer should have access to them. www.crutchfield.com or www.tune-town.com are two places who have them online.

Would it be smart of me to cutout the connections in that faceplate for the serial and mic cords, so I have access to them from the cab

Unless you can think of a reason that they need to be instantly plug-able, then no.

Usually, the serial connection is not used in the car except for special custom projects, and there's currently nothing that uses the mic connection. When you eventually have a situation where those connections are useful, it's easy enough to open the dash and get them set up the way you can use them. But until you have a use for them, they'll look ugly sticking out somewhere, so keep them hidden.

I have a CD Changer that I haven't been able to sell, therefore I am thinking of installing this as well, any ideas or suggestions?

Ebay it. Do not use it with the empeg player. FAQ Entry.