I just started using the tuner today. It is a lot easier than the DHP for startup and getting an initial read from the PCM. I did not have to pull the radio fuse (I forgot TBH and my radio is not stock) and was able to get a stock scan. HPT has a write up on the situation I posed on the OP so it answers my question.
Are there anymore write-ups for the 04+ cars or should I be good with using information from the 97-03 write ups? It looks fairly similar for a lot of it. Also the tire/wheel ratio calculator says that my current ratio is 3.29, but when I calculate it manually at the drive sprocket ratio I get 2.93 (which is what it should be). Should I just focus on the multiplier and modify manually? My car has 225 50/17 and stock is 225 55/17 (which I have found makes the speedo read higher than my actual speed by about 3%).