Thanks Power-Tripp, I almost capped the tank breather till I thought of the potential vacuum build up. For the tank vent I used an 1/8" fuel filter, (the kind you find in the tank of your weed-eaters).
The extra port on the throttle bodies is located on the top middle. You have the 3 that comes together and leads to the MAP, then 1 extra in the middle, it's just another vacuum port I believe. After looking and some pictures of other throttle bodies (here and eBay) I found that that extra port was capped, so I think they all have it, but only CA bikes with the EVAP system utilizes it.
I took it out last night after loading a tune and she seems to be alright. No CEL, and definitely more responsive. I installed the Jardine RT-1 slip-ons, SAI block offs, and removed the EVAP system.