Is Noise From Engine Or Transmission? Help!

I got a used engine for my 96 S10 with a hundred forty thousand miles on it. After I put it in, the first time I drove it I noticed that, under moderate acceleration, I would hear a knocking noise. At first I thought it was the engine lower end, but I discovered that if I give it more acceleration the noise goes away. Also the noise seems to have the same pitch as the noise my transmission used to make when it was in neutral with the clutch out. I discovered that the pilot bushing was shot and that was causing the noise. So I'm wondering if the noise is caused by my transmission, which does have 236,000 miles on it. I've still got warranty time left on this engine, but I really want to be sure that the engine is the problem before I yank It again, yank another engine, and then put that engine in my truck. Doing all that once was enough for me. And if I replace the engine and then discover the transmission's shot, I'm going to feel pretty darn stupid. Any insight you guys can give me will be greatly appreciated.