Actually, the updated shifter came in '07. Your best resource for those type of items is
TMS Intro They have a time line section to view the different options and such. Another difference is the 05-06 models weigh a bit more than 100 lbs less than the 07+ because they had to stiffen a few things to accommodate the GT500 power plant. 2005-2006 GT Manual models came with 3.55 gears standard, autos came with 3.31. 07+ GT models come with 3.31 standard, with 3.55 being an option for manuals. Other than that, off the top of my head, there are no large differences, other than available options.