Naturally aspirated, yes. Boost, no. The 5.7 pistons aren't that strong. I would recommend changing the pushrods and valve springs, they're the known weak points for the 5.7s. You can use the 6.1 pushrods, and replace all your springs with the 6.1 exhaust springs (the 6.1 intake springs have a higher installed height that requires a taller valve). From what I've seen, ~ a .560 lift cam is the highest you can go with stock heads before the guides have to be clearanced. As far as MDS goes, you can leave the stock MDS lifters in, as long as you don't go to radical with the cam.
As for intakes, you've got three options. The Mopar performance intake, which is a $1,000 piece, the XV intake, a $600 option, or you can go with the INDY Mod man intake, which is $400 if I remember correctly.
The 6.1s are great motors, but still very expensive. I got my 5.7 for $400 with less than 100,000 miles on it. Deals are out there, you just have to know where to look.
Oh, and don't forget your only two options for exhaust. Well, three I suppose. Modify the stock manifolds (not the best option), try to find some Jeep SRT8 manifolds, or run your only option for headers, the $700 TTI's.
I believe the 3G hemi is the better option when compared to piecing together a 2G hemi, which would run you well into the 10-20k range by the time you're done putting the motor together and chopping the car to make it fit. The new hemi costs less to put in, is MUCH lighter, we're talking in the neighborhood of 250 to 300lbs here, and can make equal power. Granted, it's not as cool looking as the old Hemi, but still.
Oh, and don't forget the MSD HEMI 6 box, or the FAST xfi box to control your spark. I would recommend changing the coils to the 06 and up style that didn't use any wires going across the engine. 03-05 used a traditional wasted spark style system that had wires criss-crossing all over the motor. Not pretty.
