Sure sounds like the M/C went bad as you surmised and one side has to have way lower pressure for the light to come on but from your descrip it is a part time problem that comes and goes . I suppose it is possible that the rebuilt M/C is bad. I'd give it another good visual from head to toe & have a helper work the pedal with you underneath & I'd cap the M/C with a pair of brass inverted flare plugs from the "Edelman" fittings cabinet at your parts house & if the M/C is good and bled out with it capped it will be rock hard with virtually no travel & stomp it hard and try with light pressure & see how it acts. Holler how it goes.