Possible vacuum/exhaust issues and transmission

I'll try and be brief, there's much to explain. The car had been sitting for over a year when purchased. Transmission and complete rearend had been put in car at time of being parked and never test driven. It wouldn't run. I had transmission seals put in, repaired exhaust manifold and replaced gasket. Since then have gone thru a series of replacing parts and clearing codes. CCRM, air filter, fuel filter, pcv valve, all vacuum lines, both oxygen sensors and a new catalytic converter. Most of this was due to poor operation of vehicle. Sluggish, poor idle, blowing black smoke out the rearend. Etc. She runs like a new one almost. Before replacing the cat converter, the operation was horrid but the transmission worked just fine. Since putting it on, the car won't go into high gear, the code said input shaft speed sensor, replaced it. Still it isn't changing buts runs out wonderfully. Although I feel like theres some kind of vacuum issue. The blower wasn't working for the heater/ac and in working on this, I moved the selector button. Vent, defrost, etc, what I found was an extreme draw on the engine, almost to the point of choking her out. I know this happens whenever you turn the ac on but I've never had it happen on the vent/heat side. Could this be a vacuum issue? Could this have anything to do with the transmission? I've checked for any kind of leaks pertaining to the vacuum, including under dash, since the heater controls use vacuum, found nothing. Could the failure to recognize the new speed sensor be related to the cars computer? I'm bumfuzzled and it ain't a purty sight. Lol. Any and all ideas or recommendations would be greatly appreciated. Thank you in advance