you should have three lines coming off the stock intake unless you have removed them and plugged them off. one is to you fuel canister purge, one is to the valve cover vent tube, and one is actually on the air filter canister for you stock bcs.
also look into the how to section and look for the vacuum line diagrams we have. our cars some with a ubber gay setup that ties the bov and bcs together. remove all the extra vacuum lines and then perform a boost leak test.
I know on this last ETS kit I installed I had severe boost leaks but non of which were my install. it seems that the tb elbow pipe had a fracture in the pipe at the flange and had two holes in the welds around the flange. I talked with Michael at ETS and he is going to send me a new elbow and appologized for the issue.
your not venting your 1g bov are you? they leak and cause all kinds of problems which is why I just switched to a hks.
do a boost leak test and see what you find.