You're not going to see the same max boost in x gear as you will in y gear. It's just a limitation of how Subaru's boost control works. You can get damn close, but it'll never be perfect. If you have it set to make target boost perfectly in 2nd gear, you'll probably be way over in 5th. Per-gear compensations can be done with a Group-N ROM, but that's not something you want to be touching if you're new to tuning.
Also, you'll need to be touching more than the target boost tables. WGDC tables will need some tuning as well. You mentioned this was a newly rebuilt motor. I would definitely NOT run much boost until it is broken in. I hope that you've been doing that from the start of break-in...
I would recommend you start by reading and understanding this:
http://www.romraider.com/forum/viewtopi ... =25&t=1814And in the future, there's usually a lot more help with tuning-related questions on the RomRaider forums.