Thanks man,I kept the car at the shop and see what they decide. I found the MSD 6A digital ignition with SS coil from summit racing, I can get next day ship for free for 229$ together. Then just going to run the AEM boost solenoid (97$) and just wire the 2 wires into the EMS and run it that way to get rid of any boost spikes. But they told me not to buy anything until the tuner comes back and checks it out.
So figured upgrading the systems will be best all around.
edit: offtopic,but will removing the EGR valve gain any power? or anything else I could do to gain hidden or lose power. Im kinda afraid of getting the unorthodox crank pulley.