Rod, It's not common from my experience for them to align the subframe. That alignment requires the bolts to be pull and the positions douls put in place. Ford is the only shop that I know of who would have the tools to do the job. I'd take it back to the place that put your Transmission in a tell them that they did it wrong. If it was Ford make them fix it right this time. The Lower control arms are bolted into the subframe of the car so proper alignment is key to having proper steering control and even tread wear. The transmission shop should have know about this when they did the rebuild and charged for it to be aligned since it needs to be. At the very least they should have recommended a place to do it properly. It's just very unprofessional if you ask me.
Also it sounds to me that the O2 Sensor wasn't plugged back in either way. The exhaust does have to be disconnected for the subframe to be dropped. So it's very likely that they technicain was in a hurry to get it done and missed it. Did you pick it up on a Friday?
*Edit*
I think the PO codes are just for ODB2 since yours is ODB1 you might need to find those.
