Does the PCM control line pressure...
The only other pcm controlled parts in the trans are the three shift solenoids and the tcc solenoid.
I have the kit waiting for me to install it and when I do I am going to install a pressure gauge before I even start the car, then I will apply and take away vacuum to verify line pressure response.
IMO I wouldn't drive the car until it's fixed, it may already be too late.
If you're slipping through all the gears like you say, then the vac mod kit was not setup correctly. There have been many posts here recently about whether or not the vac mod kit is plug and play or an easy install. I'd say your trans shop may not have had that much experience with vac mod conversions.
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