You're actually not dropping that much fuel pressure but you also don't have a lot of injector head room to cover for it. Even if it maintains 80+ psi, you'd probably run out of injector in negative DA as it stands.
With that said, I would add a single bap plugged into the slave fpdm. That'll fix your fuel pressure issue for the time being. You might have to add a 2nd one when the air gets cold if you stick to this configuration. You can also target higher fuel pressure during WOT operation but that'll just cause the fuel pressure to drop faster once pump flow is mechanically maxed out.
Your bypass valve is also on the verge of triggering a limp mode condition. This is typical whenever pushing over 21 psi of boost. As you mentioned, it is just an srt4 throttle body after all, not really designed for this use case. There are companies out there that sell modified bypass valves with a stronger motor. Either lower boost or upgrade your bypass if you want to avoid future frustrations. You could also take a chance that another bypass might be a little stronger but it could also be weaker. I don't recommend that route for you given where you're at with this car.
Your 1-2 2-3 short shift issue, that's weird. It's not skipping 2nd gear though, it can't physically do that, but it's triggering the 2-3 shift right after completing the 1-2. As to why, I couldn't tell ya. It's not something I've seen before which would be kind of odd don't you think?