Not being able to launch above 4500 sounds like standard behavior. I know my '95 Saturn won't rev above 4500 when it's sitting still, and it says so in the owner's manual. I don't recall seeing that in the Sonic manual and can't find it at a glance, but I haven't had time to read the whole thing yet. I wouldn't be surprised if it's a feature that they just didn't mention because most owners won't ever find out otherwise. I haven't tried revving mine that high out of gear, so I don't know for sure if it's normal.
Regarding the 3rd and 4th gear WOT problem, I have no idea. I would talk to Trifecta.