My engine would intermittently stall problem gradually got worse?

Ok so I replaced the transmission and shortly after that my engine would intermittently stall. The problem gradually got worse with failing gauges and then no start unless the gauges were working until eventually they no longer would work either. Replaced the ecu had it programmed at the dealership. But still no horn no wipers NO LIGHTS WHATSO EVER FLASHERS INCLUDED. Alternator doesn't charge either the. Only light is have is the 3rd brake light that's it. Also the dash lights come on when the key is turned on even when they are supposed to be off and my truck is also misfiring on a cylinder or two. The crazy thing is on the way to the dealership for the programming it all of a sudden the engine ran like it was supposed to no misfire running great. Until I get there turned it off and when I started it again back to the same things. IVE CHAMGED THE FCM AS WELL AND STILL NO LIGHTS NO NO THING THE ONLY THING THAY IT DID DO WHEN I HAD THE ECU PROGRAMMD WAS TURN THE NOISY DINGING OFF. EVERYTHING ELSE IS STILL AS IT WAS. Help!