That's a huge drop in power, it should not be that drastic from the addition of a FMIC. First of all, go through the entire system and make sure you aren't loosing boost anywhere. Sometimes leaks can show up and not be very noticeable and rob you of power. If no leaks, and you want to use the same core, you need to up the boost again to at least where you were before. That is a really big core and it is causing you to have more then normal pressure drop. How are your IAT's now? If the intercooler is functioning properly and your IATs have dropped substantially, you should be able to bring the boost back up to 15psi and add some more timing into the tune. That's where you will see your power increase.
There have been mixed reviews on the cxracing intercoolers. When you were doing back to back runs on the dyno, did you feel the end tank on the cold side of the intercooler? If it feels warm to the touch after a run or two, the intercooler is just not a very efficient core. You shouldn't have to wait no more then 3-4 minutes to do back to back runs on the dyno without worrying about heatsoak of the intercooler. Just some things to look at.