Problem solved! It is now loud as hell with the gain hardly up on the LC2i or amp and clipping only blips on really hard notes.
The problem was I had the plug-n-play adapter from TechnicPNP.com connected to the amp that powers the door speakers, which most likely had the bass frequencies already crossovered out. I connected it to the other one, and it's 100x better. I now regret buying the ported box, but may still use it since it's black carpeted and will match the trunk better.
I think I need to do a re-cone on the sub, I am getting a tapping sound when the sub is pushed hard. I had the same problem when it was in my BRZ on the Soundstream amp.