If it's just the fronts and not the rears, I'd also look to the proportioning valve. I would think that pedal travel or seating issues with the MC/Booster would translate to the rears as well (although maybe not as noticeable, depending on if they're out of the adjustment or not). Sounds like the guys know what they're talking about though - and your advice about the Bronco calipers says you know quite a bit about the brake system as well.
I'm anxious to hear how you get this resolved, since I'm getting close to plumbing in my brakes from scratch. Initially, I'm going with a stock set-up, but will switch over to rear discs after everything's all broken in and I'm used to the car's characteristics.
The big X factor here is the ebay kit and the red flag is having to cut the pads. I know it may be tough to hear but I would get some factory or quality aftermarket calipers and pads before I went any further.