2004 Hyundai Tiburon GT 2.7 v6, 4 speed auto w/ acceleration issue, why?

What is your question?

My Tib just began loosing acceleration. It feels like a compression issue and I'm getting a #5 plug misfire code. I've checked the coils for spark and the plugs are new, as well as the wires. When I am in drive and go to pull onto the street from a dead stop, it takes about a min for it to reach cruising speed. I've also noticed it seems as though my tranny is 'stuck' in 3rd gear. 1st & 2nd are slow to accelerate,but once into 3rd it's easy cruising until I have to make a stop. But the car is shifting through the gears. However, it seems to run up to about 3000- 3500 rpms before shifting sometimes. I've recently replaced TPS, as well as Neutral Position Safety sensor, so I'm ruling those out. I've also just checked and cleaned the Mass airflow sensor while troubleshooting which actually helped my fuel efficiency, but made no other noticeable difference. Someone suggested a fuel filter, but as far as I know, Tibs don't have inline ones. So as for the in tank filter, I've actually replaced the complete fuel pump assembly a couple months ago.