HELP!!!?

ok so here is my long story and the issues. First off i replaced the engine in my 2000 pontiac grand am back in 2007 with one from a 99 chevy malibu. The knock sensors are different and i want know if i can use the one from the grand am on the block from the malibu. Then my AC doesnt work and im not sure why. Ive used the dye to try and find a leak but there isnt one and i get no cold air but it does blow. My tranny shifts hard at times. I tried changing the filter and replacing the fluid but not too much of a difference. I also have an overheating problem that comes and goes. And lastly i had a problem where the battery would die while driving. So i check the alternator, starter and the battery. They are all fine after getting a new battery. But it seems as though there is still something draining the battery. Right after replacing the battery i had the system checked again and the battery was only reading at about 12.3 volts. Im at a loss for what to do.