Yes, you probably will need to adjust the base boost as it is determined not just by the spring setting of the actuator, but also the back pressure from the exhaust which helps keep the wastegate shut. Performance exhausts for turbo cras generally reduce the back pressure to help the turbo spin up quicker. Thus your base boost will probably be lower than before you fitted the exhaust.
I picked up on Mark's comment about base boost when a similar thread was on before - I have a JT 3" front pipe on my GM900T and noted that when a pressure gauge was fitted I checked and noted that my base boost was at stock 0.4/0.5bar so hadn't changed. It did however tell me that the APC was knackered! and I had been running a LPT for some time. All is now restored to get the benefit of the stage 1 upgrade.