My set up when similar to yours was yeilding similar boost numbers as you at 5500 with a slipping belt and the stock SC inlet. Once the belt was tightened i was seeing closer to 8 and 9#'s at 6000 rpm's.
Are you using the stock tach to judge rpm's? I have found mine was reading higher than the motor was actually turning.
Anywhich way.... You should see lower boost with a better intake manifold.... and thats a good thing

More effiecient = more power with less heat.