Transmission problem
1996 Ford Bronco V8 Four Wheel Drive Automatic 4979 miles

I put a new 302 crate motor in my 1996 Ford Bronco (302) 5,000 miles ago, as well as a new heavy duty radiator and water pump. All fluid levels were checked and all in proper range. I'm assuming there may be problems with the new engine but I'm now questioning the transmission or the new radiator as well. Before making the 900 mile trip from GA to PA all fluid levels were checked again. The new motor was making a sound whenever I stepped on the gas pedal similiar to being in a low gear but still driving at 65mph. Although the tach and other gauges are working and registering properly the noise continued to get louder during the trip. However, it goes away the second I take my foot off the gas pedal and returns immediately with the slightest pressure back to the pedal. I finished my trip, checked the ATF (after warming the engine and while in park) and it was a little better than a third of the way up the dip stick and full of bubbles and more on the brown side than red or pink. This tran. does not have a drain plug. Bottom line, 1 - what could be causing the engine to sound like it is "straining" even though all the gauges indicate all is fine; 2 - the radiator is new (which doesn't mean it's good) so what is the possibility there is a hole in the coil running through the radiator causing the bubbles and color and how can I drain it if needed without pulling the pan; and 3 - could the noise I'm hearing be coming from the trans. as opposed to the engine. PA is not my home. I hesitate to spend good money after bad and take the Bronco to a trans. shop here to have it flushed only to find that the radiator might be the problem. Any help would be appreciated.