Brake thoughts,strange things???

I cant find my posts about my brake upgrade(Cryo/drilled/slotted/EXtreme truck&tow pads) before I left for Ouray.Anyway,I was towing my trailer(2300# w/ elec brakes),and I smoked the brakes coming into Teluride.After that they felt weird at elevations,on Wednesday we changed out the rear flex line(SS/already did the fronts before going)!Pumped about 2 quarts of new fluid thru them.Seemed better until hitting alltitudes??The pedal got softer until returning to a lower alltitude.I took my infrared thermometer with me and took readings constantly.The original drop into Telluride was a learning curve.But everything after that was strange,dropping into Black Bear was a little uncomfortable along with the thought of the drive back down thru Durangnly thing we can think of was lack of vacumn??Any thoughts??