As always, do the easy stuff first. Pulling a transmission sucks, especially if you discover you didn't need to.
It doesn't sound like transmission to me, more a cable or clutch problem. We're it me, I'd re-install the adjuster correctly and then put a new stock cable in it and go from there. There certainly appears to be enough other evidence on the car of someone simply not knowing what they were doing while modding it.
I'm not suggesting this is your issue but merely something else to look out for - years ago I had several fingers on a pressure plate go bad and I experienced the same behavior you're describing. You would be able to see that through the inspection cover on the bellhousing.
I think you are right, I think the initial owners put a lot of great parts on the car... and I keep finding more and more each time I work on it (full sub frame connectors the previous owner didn’t even mention.). That being said the most recent owners seem to have been in over their heads with the car.
I obviously know the firewall adjuster isn’t correct so that needs to be reinstalled and I might as well put a new Ford cable in at that time. I will Jack the car up and look through the inspection hole on the bell housing to see what’s going on when the clutch is depressed. If it’s a flywheel or clutch issue I’d like to know as replacing the cable and reinstalling the adjuster while necessary won’t fix the issue.