This one looks similar to yours and has similar style clamps. may help you figure it out:
http://www.youtube.com/watch?v=B0kuCpY_OqY
I also think Mike (comanche87) has a similar style and might be able to help.
You need to use the newer style gasket with it and reroute/plug some of the vacuum lines. mjeff87 did this, I think it is in his build thread. Get the felpro gasket, its worth the money. youll need the newer style black one.
If you think it will help, I can mail my 89 electrical manual to you to use. I know there are copies online but having the book at the truck may make life easier. Just send it back when your done. I also have the regular 89 FSM too if that will help.
I have the sirius replay model. I like it cause it has 30 favorites you can set. When a band comes on that you like just hit the memo button, then it asks you if you want to store the band or just the song. Then anytime that band or song comes on any station it alerts you. It also comes with the docking station for the house.
I have an automatic so I necer had this problem, but Ive read alot of threads about it. The main question is usually how to get the fuse box out. If I remember there is a bolt in the engine bay that you need to pull then the fuse box seperates into 2 halves. don't know if that helps.
What color? Theres a maroon one sitting in my garage. I don't think my buddy will want much for it. But shipping can be a bit much. Probally best to grab one out of an 84-96 cherokee at the JY if you can.
If I remember from when i did mine, just roll the window down and pull up on the wipe. The clips will stay in place on the door. Then the new clip just slides back in.
I broke a line on the MJ 2 weeks ago when bleeding the brakes after a 95-96 double booster upgrade. Then 2 days ago found another broken one on the XJ (thought it was the wheel cylinder originally). The rear line are very easy to replace. They come with the correct size fittings and they are already flared. Flaring is not hard tho.
I'm at work but I can check it a little later if you still don't have it running. You said the black wire started smoking, since those are fusible links maybe one of them got fried.