o1heavy,
A lot of guys do run the factory computer with fuel injection. Most with good results. Unfortunately some have run into difficulties, and the factory ecm is limited it its ability to deal with changes like cams, porting, and superchargers. Early centrifugal blowers had the bad habit of destroying hemi engines. Those problems have been dealt with and the kits from Kenne Bell, Paxton, etc are now reliable.
All that being said, the factory ecm with a wiring harness from Hot-Wire or Street and Performance has served many FABO members well.
If you want full control over fuel and spark you have a few choices.
Mopar Performance sells a kit, that is basically a rebranded AEM unit, it comes with an 80mm cable operated throttle body.
FAST sells a kit that uses one of their 92mm GM style cable operated throttle bodies and an adapter
Megasquirt is a DIY controller that can be fitted to virtually any engine. As a result it is NOT very user friendly.
You can cut and splice the stock hemi wiring harness and use all your factory sensors. You are pretty much on your own for wiring up your megasquirt but as you read more and more you'll come to realize that it is not that complicated, just a butt load of wires.
You will need to adapt a cable operated throttle body as Megasquirt does not support drive by wire. I made my own adapter to use a GM LS style cable operated throttle body, or you can buy an adapter from FAST for $68.00. The GM throttle body will use a common GM throttle position switch and Idle Air Control Valve.
To cut a long story short, Megasquirt is approximately 1/3 the price of FAST and 1/4 the price of AEM unit. MS is truly DIY you can either buy a prebuilt unit or get out your soldering gun and build your own. You'll save about 200.00 if you can solder.
In addition many in the community who have used both AEM, FAST, and Megasquirt tuning software actually like the Megasquirt software better.
Also and this was important though not critical, the Megasquirt tuning software is written in Java so it has been ported to Mac OS X. It was important to me as I have a Mac and although I could load Windows on it, I didn't want to spend the money on a Windows license if I didn't have to.
Here's a couple of links to get you started
http://www.ms3efi.com
http://www.diyautotune.com
Hope this helps.
Regards,
Joe Dokes