You just wouldnt be able to take advantage of the VVT. however i know megasquirt is developing capabilities for VVT now. As far as price goes they are in everything chrysler makes so they can be had on ebay for about $800. They weigh 90lbs lighter than the previous 3.7 and 3.5 v6 engines. Have to find out if Megashift will control the NAG transmissions
The megashift will run the NAG and probably the 8 speed too, but only if you do the development for it, there is not much (if any) out there in the way of chrysler standalone trans support. If you really plan to go down this road, the man trans would save some headaches. I looked pretty seriously at building a 3.6L for a project I have.
The big decision is whether to run it stock and have to keep ALL of the stock harness, modules etc. (the "simplest"). Keep in mind, you can't just cut out parts you don't want, everything is networked together, you will need to keep everything that is wired to the ECM in any way. Fuse box, any gateways, there is a ton of stuff on the CANBUS network that would have to stay. Ideally you would want everything from a totalled vehicle. If there is a donor vehicle (Wrangler man trans 2wd?) with the 3.6L you would like a wiring diagram for, I might be able to get one for you.
Or doing a stand alone would require you to research most of the control logic (Dual VVT, trigger wheel etc.) yourself. Megasquirt has great support, but more than likely you may be one of very few trying to run one of these engines and Chrysler is the worst when it comes to being open with tuning and component specs.
Some guys will comment that you can make anything work, but it's not an LS swap.
I'm not trying to discourage you from doing this, just the opposite, I think an early A body with this engine making good power would be really cool and light!. I'm just trying to illustrate some of the issues you would more than likely have to solve on your own.
Ask questions and read up on MS if you decide to explore that route
msgpio.com (megashift site)
ms3efi.com