Dave,

If you are going to keep it with EFI, the most economical wire harness would be the Tony Squier Engine Harness (Hotwireauto.com).
Tony and his son are great people to deal with who are down to earth.
The harness was $950 and if you get a simple PCM (Powertrain control module) you can get one for about $650 tuned or less if you get a good used on Ebay. I spend for a new PCM and sent it directly to Dave @ B&G for a perf program and cost me about $850 total.

The stock PCm route is very tuneable especially since now they have Diablo Sport handheld engine tuners which will allow you to tune your engine if you modify it.

I did a write up on my 6.1 swap, it is the archives 6.1 Hemi install

You are going to so love the 3G Hemi. I know I do

Feel free to ask any other questions!

I'd gladly help you walk through the swap.

I personally think your best bet for an engine is to get a BRAND NEW 6.1 HEMI from my buddy Josh @ Champion Chrysler Jeep. $4700 for the complete engine!
Add $950 harness & $650 computer and for about $6300 you are on your way to a running 6.1 Hemi engine.