Wow thanks for all the responses guys.
legallyillegal: I'm gonna head to a good shop and check them out, and also get my boots properly fitted.
BA: Yeah, I'm gonna get a proper boot fitting. I've tried tight, medium, and loose laces, nothing works. Also, I hit up the gym a lot this summer, i'm skinny but strong. I don't think it's a muscle thing. As far as pre-existing nerve damage, this is the first time I've had any nerve problems. It's a superficial nerve and it's not horrible, so I imagine it will get better if I keep working on it, moving my foot and toes around.
earl: Great info! No bumps, cysts, or swelling. I'm pretty sure it's just a combo of bad arch support and lack of a custom setup as BA mentioned. I can't think of any recent falls, except that I did fall once on a jump my last time riding (3 days ago). I hit my tailbone though :P I also probably tweaked my back. I should hit up my chiropractor.