I believe were specially recorded with no ATF signals,"
OK, so they were separate frequencies, not the carriers.
However the lack of ATF signals is not required to align the deck. You still just align it, although you might confuse the system.
Most likely with a print you can find a way to disable the ATF system altogether, even if you have to disconnect the output from the heads. Believe me it can be done and should be done on a customer tape recorded previously in that machine, partly because compatability with other machines is not likely to be a big issue. For alignment I would get the tape tension as low as possible.
You know they said you needed all this equipment to align the old VHS recorders that had pots for the FM deviation and frequency and all that shit. Know what I did ? I just coupled the record signal to a deck "playing" a blank tape and "tuned it in". There is almost always a way, and remember, they are in business to make money.