Welcome to the forum. I have a 2007 Ram MegaCab with the HEMI and no MDS.
What I've done is put in a single in / dual out Magnaflow muffler. I had new tailpipes and tips put in and with the removal of the stock muffler and tailpipe, that was the end of the stock resonator. I did not replace it.
The sound of an exhaust is subjective, however, I like the Magnaflow sound. And since I don't have MDS, I don't have to worry too much about drone. I do have some but all I have to do us turn up the radio and it's all good.
About intakes. There's two schools of thought on the closed vs. open systems. Those that advocate the open systems (a simple tube, interface with the TB, a large cone filter and some clamps and rubber sleeves) say they flow better. They are exposed, however, to hot engine compartment air.
Those that prefer the closed systems (AFE, Volant, etc) choose them because those systems isolate the intake filter from hot engine air.
So, that seems to say that if it's sucking in hot engine air, is it really a "cold" air intake? I think not.
With respects to the flow characteristics of each, both will provide more than enough air to the engine. The throttle body, intake manifold and cylinders will only hold so much air.
Programmers. Well, stay away from the Jet modules. No big gains there, pretty much a waste of your money.
I firmly believe the DiabloSport Predator is the best bang for the buck programmer out there for the MOPAR HEMI. I have two HEMI powered vehicles and have a Predator on both of them. I've seen a definite improvement on both vehicles with that tool.
With my CSRT8, I went from 358 RWHP stock to 379 RWHP on the canned 91 octane tune. After a CMR tune by a DiabloSport authorized and trained shop, it went above 400 RWHP.
And the Ram 5.7L HEMI? Here's the dyno chart with the blue lines being the stock program, the green lines are the Predator tune. Notice how the HP and torque come on sooner in the RPM band with the tool installed? This is what makes the truck move out quicker and respond better off idle.
The other key to great HEMI performance is air/fuel ratio. The stock tune runs lean, around 14.1 air/fuel ratio, and it pretty much stays there almost to redline. 14.1 is pretty lean and it causes knock retard, where the knock sensors see pre-detonation (pingin) and pull timing, robbing you of HP.
The Predator tune dropped it to 12.5 to 12.8 pretty early in the WOT run. Those numbers mean that the fuel in the mix has increased (remember, it's air to fuel ratio so the lower the number, the richer the mix) and the HEMI really picks it up and goes with a better A/F ratio. Here's the dyno chart on the A/F readings. The blue line is the stock tune, the green line is the Predator tune:
So my suggestion is to go with a good exhaust system. You can replace the stock muffler with a single in/single out. If you delete the resonator, you'll get some drone if you have MDS. Interestingly enough, the Predator can turn off MDS!
I also suggest you take a look at open and close system CAI's and go with what you like but remember, the closed systems isolate intake air from hot engine compartment air. This will improve HP as fuel/air charge is denser due to the cooler air.
Lastly, go with the programmer you want (Bully Dog, SuperChips, etc...) but in my experience, the Predator is really the best one out there for the HEMI.
Just my $0.02 (or maybe a bit more...