Boost Loss

My friend has a 2004 Mk4 GTI, He has full exhaust, Short ram intake, and TEIN Suspension, and ECU Upgrade. My question is, We just installed an EIP Front Mount Intercooler with blow off valve. we disconnected the battery and now since we hooked everything back up he is only boosting at <5 Bar, He was boosting at 1.5 bar. (17-21 PSI). The computer reset, his windows would not go auto up and down, but then started working after 10 minutes. The boost is still very low and i was wondering if any of you know what the problem is, have any suggestions, or what to do with the computer? Thank you very much.