I don't have access to my Windows PC to open up the log files right now but sounds like you're verified the turbo itself is work by disconnecting the WGA vacuum line which should allow maximum boost. So if you know the wastegate actuator (WGA) is good and getting low boost that could be caused by too much boost reference pressure to the WGA (the boost pressure in the vacuum lines counteracts the internal spring pressure in the WGA to keep boost down, otherwise you'd get max boost the WGA's spring pre-load would allow).
A couple thoughts, when you said the problem started when you removed the Mopar "BOV", was that the Mopar Performance Blue Plate and going back to stick or did you remove the factory bypass valve (i.e. blow-off valve) to install an aftermarket BOV elsewhere on the charge pipes? Are you using the Mopar Performance 3-bar sensors or the SRT-4 Caliber sensors with adapter? Have you checked to see what the MAP sensor is reading with the engine off an while idling?
A failure of the computer or problem with the tune suddenly developing would be near the very bottom of my list of things that could go wrong, so chances are it's either something mechanical (vacuum control system, WGA related, etc.) or electrical (sensor, wiring, etc.). Is the car really slow to build boost and tops out at the 8-10 psi? I know you mentioned swapping solenoids but if that's how it's running that would also match up to a problem if the WGA was getting a boost reference signal (i.e. full boost pressure from the pressurized intake side) due to the solenoid not cycling (on-off duty cycle) to limit this pressure from reaching the WGA's vacuum can, which is how the computer raises boost pressure.
Something like that could be electrical related with the solenoid or due to the computer not commanding the correct duty cycle. If that was the case there's a much greater chance the computer is not behaving correctly due to a bad sensor input rather than a software or internal PCM failure.
Eric H. - '04 Neon SRT-4 (eBlue/S2) - '92 Dodge Daytona IROC R/T
'91 Dodge Spirit R/T - '19 Pacifica Hybrid Limited - '14 CTS-V Wagon
'08 Cobalt SS Turbo - '14 Cruze Turbo Diesel - '02 SVT Focus (S/C)
'04 SVT Focus (EAP) - '07 Ram 1500 - '81 & '85 Chevy Citation X-11
'90 Pontiac Turbo Gran Prix (ASC/McLaren) - '93 Olds Achieva SCX W41