Not that I recommend a MBC without being tuned for the boost level it is adjusted to - but did you try and adjust the MBC to see if boost changed?
Do you know if the ECU is stock or tuned? Stock turbo?
When you unhooked the MBC I assume that you installed the stock EBCS in its place. You need to find out if your ECU is stock, or just make it stock. Do you know anyone with a Tactrix cable, they can try and read your ROM and run a comparison to see if it is modified or not. If the ECU is tuned with Cobb (or other aftermarket tuning) the Tactrix cable may not be able to read the ROM. In this case you know it is not stock, you just do not know what is on there.
Buy an AP now and it will install over whatever map is in your ECU. Then you can load a stock map and know exactly which map is installed in your car. [Since you are getting protuned for stage 2, I assumed that you will be buying an AP.]
It is not worth getting protuned before you install the DP and intake. It is worth finding and fixing the boost problem, though. I would do both at the same time. When you say "...I had the boost gauge installed..." I assume that means that you did not install it yourself. If this shop is a good Subaru shop, they should be able to help you straighten out your boost problem. This is your best option. It is best to fix the boost problem and then install the new parts and get protuned.
If you stay out of boost and drive your car gently, it is fine to install the intake / DP and then drive 20 minutes to the tuner. This assumes that the intake you purchased is a reputable one [Cobb and AEM come to mind first but I am sure there are others] and works correctly. Even if you need to tune for the intake, the ECU has the ability to adjust in closed loop and you will be fine for the short drive to the tuner.