Vacuum issues with 98 Ford Escort ZX2 on 1998 Ford Escort

Car had been sitting for over a year when purchased. Transmission and whole rear end replaced when it was parked. The car would not run at all. Replaced transmission seals, input shaft speed sensor, air filter, pcv valve, all vacuum lines I see, cleaned MAF and IAC, replaced both oxygen sensors and new catalytic converter. I've probably forgotten something. Cleared up all the codes that have shown a problem. The car operates better in many ways and still there's an issue. After putting the cat converter on, now the transmission will not change into the last gear. There was no problem with that before as it changed out fine without the converter, just sounded horrible. And there's something with the a/c and controls. I can tell all the ac parts are working but no blower. When I was checking this out and working the position controller of the heat/ac I noticed an extreme vacuum problem. At a couple of the settings the car almost stalled out. Very odd, I've never encountered this before. I'm thinking there's something off with my vacuum somewhere and my question is would this affect the transmission in any way. Please keep in mind, I'm a short blonde gal from the South with more than a few decades in my birthday not a trained mechanic, I just love tinkering with 'em. Thank you in advance, GypsyLou

Asked by for the 1998 Ford Escort