1990 Chevy Silverado Can't seem to find the problem.

I have a 1990 Chevy Silverado that we put an engine from a 1993 Silverado 1 ton standard transmission, in it a year ago. The truck ran fine until a month ago I was about 10 or 15 miles from my house and I stopped at a stopsign and it just died. I got it started again but I had to press on the gas to get it started, and it would just die everytime I had to stop. I drove it another 8 miles with one foot on the gas and one foot on the brake( when I had to stop), until I got to one red light and it just died and would not start again. We have some extra parts for the truck but nothing helped sometimes it would run fuel through the injectors and sometimes it wouldn't. Anyways we changed the diaphram in the throttle body, we changed throttle bodies, and we changed the TPS,and the IAC, the EGR valve, and the fuel filter and the MAP sensor, some seems to help in other other areas except the problem remains. 2 days after I have my truck towed home, it starts right up like it has no problem, but if you go more than 20 miles in it , it will die everytime you have to stop unless you have one foot on the gas and one on the brake. We did however change the fuel pump a few years back, but the truck set for almost 3 years with no motor in it and 3/4's of a tank of gas with no fuel stabilizer in it. We did pump out the gas that was in the tank before we got it running again, but I'm not sure if we got it all. My husband recently pumped out some gas when we started having trouble and it was brown like used oil. Please Help!!! Thankyou.