You are doing an (nearly) identical swap as I.
You have the wrong sender in the Atlas. But it shouldn't be a biggie. On my settup, I've got the Autometer speedo in my TJ, using the Autometer sender that came with the speedo head. I'm (planning on) using a Cherokee sender from a NP231 (mechanical sender, wrecking yard, $10) that adapts over to the electronic sender from the Autometer unit.
(edit- so I walk out to the garage, and look at the sender that Autometer gave me, and it's a two wire sender. The Cherokee I got the sender is a hybrid-electric-mechanical thingie. It's exactly like the early ones that were strictly mechanical, but with a electric two wire sender added to it. Much like the sender from Autometer)
I too got rid of all the TJ wiring and brain.
Another option, is the TH350 tranny should also have a sender (for the 2wd version) and you can always install a sender in that position and bypass the T-case completely. Yeah, you won't be accurate in low range, but who cares? However, you'll probably have to pull the transfer case to install the drive gear.
I'm not streetable yet, so I'm not totally sure my set up will work, but I really think it will.
Also, I've got a really neat dash cluster. See this link.
Link -->
http://nw-wheelers.com/forum/showthread.php?t=12840
Tony