antilock brake bleeding?

I have a 2001 dually diesel It was wrecked and the mastercylinder resevoir was off for 8 months we have bleeded brakes and antilock system at lines. The antilock and brake light will go out for a while then come back on then go out again also you can feel antilock system come on. The rear adjusters are working on rear wheels and adjustment is fine. Does the proportioning valve have to be replaced or reset? I took it to the Stealership when trans wouldn't shift also telling them to check why the brake light was on and they told me trans needed rebuild and wanted $2400 for a new trans not saying anything about brakes. I bought a used trans off ebay and installed it and it didn't shift either, Then I pulled wire off proportioning valve to get the light out and the trans shifted fine!!!!. Ripoff dealerships!!!!