As far as power delivery goes, there is not a thing wrong with the early Hemi's. Yes, the later ones are somewhat improved, but you can't EASILY upgrade yours just by using a lot of later parts. Some have replaced the cylinder heads and intake with the later (so called Eagle heads/manifold) units, but to gain the full benefit you'll need some sort of header back exhaust system and a better camshaft. There are other subtle changes that you'd have to address, such as the emissions EGR Valve.....the early ones have it the later ones don't. You wouldn't be able to "adapt" the VVT system to the early one either. On mine, I just advanced the cam a fixed number of degrees and that's the way it is all the time.
If you're after more power from yours, IMO, you should address the weakest link first, which is the exhaust system. A good header back system would be a must. I had a completely custom header back system built about 5 1/2 years ago and it really wakes up the Hemi. I've also done a bunch of other stuff (see signature below) that has boosted my horsepower by quite a bit. I've taken more than one full second off my quarter mile time as a result.
The weakest engine component on the early (05's and 06's) Hemi's is the possibility of dropping a valve seat. If this happens, at the least you'll have to replace the head, and at the worst, the whole engine....or at least the piston of the affected cylinder. I have two "early" Hemi's, an 05 and an 06, and I've not had a problem....knock on wood. This seems to be aggrevated by overheating. On both of mine, I've installed 190* thermostats (203* is standard) and set the fan to come on beginning at 200*. The stock settings begin turning them on around 225* or so, IIRC. In any case, I don't lose any sleep over it, but if it happens I'll just have to build the engine the way I want it. If you want to be relatively certain this won't happen to you, change the heads and make sure they have the new valve seats in them.....cost for a "good" set of heads is around $2000, and will give you only about 30 hp.....if you have a good header back exhaust.
IMO, the best bang(s) for the buck(s) for the early Hemi are, in this order: complete header back exhaust with a 3 inch straight through cat. back (I paid $1400 5 1/2 years ago); a good aftermarket MDS compatible camshaft and kit (I paid ~$600 for the cam and kit and another $200 or so for special tools and tensioners); a good tuner, which costs around $300. I prefer the Superchips WITH the "Advanced Transmission Tuning Application" SOLELY because it allows me to totally control all up/down shifts and torque management settings. Just remember that most mods., by themselves, don't make a big difference, but cumulatively they all add up. Also, if you go overboard on any of them (such as too radical a camshaft) you'll end up adversely affecting driveability, especially on the low end where the vehicle is driven the most.
Good luck on whatever you decide to do, and welcome to the forum.