Check out these sites for good info
http://www.cumminsforum.com
http://www.dieseltruckresource.com
Lots of good info there
The only thing I will say is if the modding bug bites you and you start adding power, other stuff will need to be upgraded.
3rd gen Cummins (03-07 for the 5.9s) can make 500 hp with a programmer and box stack. Probably about double the hp of the 7.3 with a chip.
Obviously stock autos and stock clutches don't like 1000 ft lbs to the rear wheels.
I have an 03 auto and like it. A good valvebody and torque converter makes a nice difference. I also had an 01 6 speed and had a Southbend clutch in it. Pretty much will take anything you can throw at it up 500-600 rwhp.
You see a lot of Dodges with the manuals. Having had both, I will say the auto with some upgrades is great. Maybe if I was towing 10-20k consistently I would say the manual is a better choice and I would switch.
None of the 03-07 trucks are very problematic. Typical front end wear items (seem to be the same for all HD diesel trucks), and maybe injectors being more failure prone then the older trucks. Especially the 04.5-7.
03-04.5s have problematic lift pumps which are easily fixed with an aftermaket lift pump. Like my Airdog personally.
03-04s have a smaller turbo and a little less power (HOs are 305/555 vs 325/610) but are known for better mileage.
04 has Tow/Haul auto but is really just OD lockout
05 gets better shift patter for Tow/Haul but no OD lockout.
Some 05s have plastic intercoolers.
06 has OD lockout and Tow/Haul
06 has different headlight and interior. Although I like the 03-05 interior better.
07 has different badges