2004 wrx tranny swap

hows it going subie friends.. I recently purchased a 2004 wrx and have had it for a few months and since i have had it the syncros in first have been pretty worn, along with the clutch. So I decided when i did the clutch I would do the tranny as well (since I found one for a good price). Turns out I accidentally bought a tranny with a push style clutch set up as opposed to the pull style I took out. The conversion was actually pretty simple just needed a different clutch and flywheel and a longer hydraulic hose for the slave cylinder. Anyway we finished putting the car back together and the car had a extremely bad vibration (we thought it might be the center dif gears binding up since it shifted well and also did it in neutral too). However, after driving for a few miles the vibration has gone down a significant amount but is still there (pretty sure the trans is shot, and i do not believe it has to do with flywheel or clutch misalignment because its not consistent with the revs.) And the other thing that has me scratching my head is after we put it back together is the motor is sputtering out at around 4500/5000 rpm but the only thing that's different is we didnt plug the speed sensor in because this tranny is a little different and doesn't take the same speed sensor and also we caped the whole where the o2 sensor goes (but the code for the 02 is deleted anyways) any knowledge regarding the vibration in trans and the motor sputtering out would be helpful thanks.