Your reasoning is mostly sound, but I have it figured a bit different.
First of all, I have the opening scene of Future Shellshock taking place in 2006. I know that doesn't jive with the "100 years in the future" thing, but I always took that as rounding up from 99, which isn't ridiculous to assume. I even remember the old ninjaturtles.com synopsis for The Journal stated that 2006 was the year they were sucked into the future.
Other than that, it looks like you've added another year because of The Christmas Aliens. Production order, original airdate and DVD release are all over the place, but I place the Christmas special in the season 2 era. Makes sense there since the gang members weren't using Triceraton guns (like everyone was post World's Collide), and Leatherhead was still missing. So Christmas Aliens and Golden Puck would have been the same Winter.
Here's my whole timeline, if you're interested:
http://forums.thetechnodrome.com/showthread.php?t=34184