get a pro tune and ebcs. when you drop it off to get tuned tell them you want this issue resolved as well. Then if it happens again, its on their dime. Don't worry about upgrading the intercooler until you upgrade turbos or are pushing your stock one to the limit. yours should be fine with just stage 2 and a pro tune. You will love the pro tune compared to ots maps anyway and its better for your engine. They should also be able to set up your bpv perfect as well. It will be money well spent!
06' wrx tr