1997 Dodge Truck Engine popping

Engine Mechanical problem
1997 Dodge Truck 6 cyl Front Wheel Drive Automatic 150k miles

My truck has a rebuilt engine installed last year and very few miles driven on it. I stopped driving it due to very loud popping in the engine when accelerating.
This week I took it to a mechanic because I thought the fuel pump may be bad, but instead he found that the 4th cylinder was not firing and repaired that instead.
Bringing the truck home, the check light is on and the truck stalled several times and would only start after banging on the gas tank. (Fuel pump)
My concern is the popping in the engine has come back now that they repaired the cylinder. He says it's a transmission problem, most likely the torque convertor, and that liquid is pooling in the transmission. I don't get it.
I'm taking the truck back to have the fuel pump replaced, but if indeed the transmission is causing the loud popping in the engine when I accelerate, then would it be a waste to invest any more money in this truck?