I think I got it figured out now. First, I had some gain issues with my interface. Now that that is fixed, the rta works much better. I attached my frequency response after tuning. I used the rta to level it out as best I could, then used the sweep technique to notch a couple frequencies that sounded bad. You can see a bit of a notch at 130Hz, where my crossover is set. Ill attribute that to the alignment discussed earlier, but i don't really have the gear to fix it now.
Oh, and I think the roll off at the top is due to the radioshack meter I'm using. Every one I've used does that.