ugh... I have posted this SOOO many times.
For the sake of my sanity, I will modify the above until it is correct. EVERYTHING in this post will be 100% correct, for any future lookers.
1. '03 and '04 come with a 7/70 factory Powertrain warranty
2. '04s with build dates prior to 01/31/04 possibly had cam bolt torque issue.
3. Some '03s had valve Back-Cut issues (some of which were corrected at the factory).
4. '04s and up have a different oil pressure, and Oil Temp gauge (Wider sweeps)
5. '05s and up have a slightly different factory head unit
6. '05 and up have slightly different valve covers (vent tubes are at the front as opposed to the rear on '03s and '04s)
7. '04 and up came with a trunk mat (you already mentioned this).
8. Factory oil fill on '03s and '04s is 10W-30 and 0W-40 for '05s and up.
9. No special editions (i.e. Mamba's, VCA editions, Copperheads, Commemoratives) made in '03.
10. 2003's have different connecting rods than 04+. They are forged in 2003, and PM in 2004+. Crank balance is also different.
11. 05+ has dual knock sensors and thus a different PCM.
12. Crank Trigger location moved from the flywheel in 03-04 to the side of the block in 05-06, like the 92-02 cars.
13. damper bolt changed in 2005+ back to the 3/4" thread from 92-02, VS the smaller 13mm used in 03-04 that was problem-prone to backing out.
14. Main Bearings changed in 2005 to 180 degree mains from 120 in order to adress oil starvation issues at the rods. this accounts for the lower oil pressure at idle seen in 05-06 cars. THE OIL PUMP AND RELIEF DID NOT CHANGE, NOR DID THE CLEARANCES.
15. early 03 cars are problem prone to rear diff carrier shaft failure. easy fix, replace the shaft.
16. 04+ cars have red calipers.
17. timing cover changed in 05 to incorporate a wire holder for the cam sensor. older covers used a bolt-on "clip"
Thats all I can think of right now, but I think I covered some of the more technical ones that not many people know for SURE. I am SURE on these items, I have dealt with ALL of them first hand.