The cluster mileage reading will either be all dash or a mileage. Since the cluster displays mileage and the ODB2 scanner is talking to the PCM, this confirms the PCM is working at some level.
This also adds to the theory the problem is a pure PATS issue. What bothers me is how a car that worked before the motor swap now has a PATS problem. What has changed?
As has been mentioned before, a blown F2.34, F2.21, F2.5 F2.37 fuse could "create" a PATS failure.
There are other fuses in the battery juncion box that "feed" the CJB. So a blown upstream fuse can be the root cause.
The OP states that the fuses are good. However, I have personal experience when troubleshooting a problem. 1st item was to "check" the fuse. We were wrong and thought it was good when in fact it was bad. What followed was 24 hours of wire harness trouble shooting that I will not soon forget. All of it preventable.
I will never just LOOK at a fuse ever again.
Knowing what I know now, I would pull fuse F2.34 and verify there is +12 volts with the key on to the supply side of the fuse. This is an important step because it confirms the upstream devices as well.
I would test the fuse with an Ohm meter. I wouldn't just replace the fuse. I would want to know what the fix was.
I would verify +12 volts on the TPS and IAC red wires with the key on. This confirms the motor's VPWR circuit.
I would verify +12 volts on several COP's WH/LB wires. This confirms that the ignition circuit is hot.
Best to use a test light that will "load" the circuit.
Another theory is that due to the long time this car has been setting, the PCM or the cluster has "forgotten" it's programming. In this case, disabling PATS, locksmith, or dealer are the options.
Regardless, the codes stored in the cluster will provide important clues as to why PATS is not allowing the car to start.
F1=BJB=Battery Junction Box; engine bay
F2=CJB=Central Junction Box; Driver's kick panel
>>Edit for completeness sake here's the information for the 1996-1998 model year 1996-1998 BJB & I/P Fuse panel layout https://www.allfordmustangs.com/foru...fuse-help.html