I know I've not been much help to you
As for the fuel pressure reference ....
I'd not be able to comment about that as I just use the OEM regulator
and my need to know the pressure has never came up so I don't
have a gauge
I've never looked at any vacuum readings on my 95GT as well
When dealing with Closed Loop, I kinda used reference points such as
pulse width, load, kamrf, lambse, maf volt, and such
If you have not set your fuel pressure back to OEM value
Maybe that would be a place to start and see if things change
My first thought would be a leak of some sort
I did see you got new O2's but if you suspect one of them
You could switch em and see if things change
Grady