Corey,
One thing came to my mind... narrowing this down more. What do the plugs look like? Do they appear rich/lean? I guess what I am saying is that we do not know if this is a fuel delivery issue or a electric issue yet. Basically your motor is operating similar to lack of overall throttle... but not sure yet if it is a spark problem, or fuel issue directly/vacuum issue... I have chased my tail many times bouncing all over from one suspicion to the next w/o being certain of where I started.... it does sound like your box is lacking delivery of spark @ WOT as a possibility... I wonder if you have a vacuum problem of some kind; or lack there of.