I'd go Gen III Hemi. I picked up a 2008 6.1L with NAG1 trans, all accessories, computer and wiring harness out of a Magnum for $4,000 off Ebay. If you don't mind messing with the wiring, you get EFI, a good charging alternator, power steering, and A/C. I also got the OD trans, but the trans computer part is still a sticking point. A manual overdrive trans should make the conversion easier?
I also see the new crate 6.4L Hemi engines for $7500?

I basically got something like this, but with lower miles:
http://www.ebay.com/itm/2007-07-Dodge-Charger-6-1L-Hemi-SRT8-Engine-Auto-Transmission-108K-OEM-LKQNW-/272049647319?hash=item3f576c2ed7:g:JNsAAOSwpDdVBDCd&vxp=mtr

Like this place (may even be the same?) they have make an offer, when I offered $4,000 I didn't think they would accept the offer, but they did?