1995 Honda Civic DX 1.5l 16 valve non-Vtec A/T

I recently got done with a port and polish as well as doing a custom Cold-Air intake system on my car.
I took it out for a test-drive, and the shifts seemed to be high. And not shifting when it should. Normally, the car shifts automatically at 45 mph from 3rd to 4th gear when crusing. It's only in 2nd, and doesn't shift out until about 60 mph, 2nd gears redline point. I think that it's just the computer re-learning it self, for the battery being disconnected for so long. Also, I suspect that I may need a Transmission flush. Any help?