So I have seemed to have fixed my over boosting issue. Contacting COBB a few different times came up with a few different options to fix the problem.
1. Load the WGDC (Low-WasteGate Duty Cycle Map) which come to find out they do not have for the 04' WRX, so that became a non-option.
2. Load the Stage II 91oct map instead of the 93oct.
3. Manually adjust the Wastegate Actuator Arm 1/2 to 2 full turn max out torwards firewall to create lower boost.
4. Make sure I have no leaks in any of my vacuum lines and check all connections.
Well it seemed to be a combination of 2, 3 and 4. I used electrical spray cleaner and cleaned out all the hoses and lines from the BCS, which I noticed a small amount of oil residue on the exterior of the hose. Flushing them out showed they did have oil residue inside and were pretty dirty. Also cleaned out the BCS.
At the same time I went through and made sure there were no leaks or lines leaking or not fitting correctly. Everything seemed good with this step.
Last I adjusted the Wastegate Actuator Arm out 1.5 turns torwards the firewall. This brought the boost down to a smooth 14 to 15.8 psi with no surging or over boosting. I then adjusted it back in 1/2 turn which has put me right where I am supposed to be at 16 to 17psi. Things seem to be running smooth with no over boosting and no surging as well. So I hope this has fixed my issue, and thanks to all who tried to give advice and help with my issue. I will be installing my catless uppipe this week as well so hopefully everything is running well after the install, I believe it should just give me quicker spool but there may be other benefits I am not aware of. Thanks again.