Metal Monkey, if you haven't already make sure you get the brake line at the back that goes from the drive shaft tunnel to the rear axle............these get forgotten on live axle cars. My original thought was the hoses, hopefully this fixes your problem.

I'm feeling your pain............I went to Friday night practice at the Kart track and during the 3rd session the pedal floated down to the floor, I spent Saturday getting it sorted and the Kart only has a single master cylinder one caliper....mighty-vac did the trick.

Tom