I have a line on a 2004 4.0L GC engine with wiring harness and computer, my questions are this, which tranny and transfercase should I use and what else will I need, will ym current gauges work or will I have to do a whole new dash?
Well, it's an OBDII engine. If you have a TJ then it will make things easier. If it's a YJ then it can be a pain unless you either convert the Jeep to OBDII or convert the engine to OBDI.
I'd probably use the 42RH that comes with the grands. It's a good transmission and is used today still. Otherwise you could do any number of swaps. You will not be able to retain your transmission though. With the transfer case you have two choices. Either use what it has (probably quadratrac) or use your 231 (with input shaft change) or go with a Rocktrac from a Rubicon.
Depending on your Jeep, your tach will probably be off and you'll need to replace it. Either with one from a 4.0L or aftermarket.
Have you thought about the radiator any? You'll also need to find or make some frame engine mounts as the 2.5L won't match up.