Had to get another transmission. So I did both. Engine pull, then after the trans wouldn't work, I had to pull the trans and replace it. Replacing the transmission was harder then pulling the engine. Had many problems getting it all lined up.
Transmission is in and it shifts and goes down the road. It makes some strange noises, even at idle though. Sounds almost like a rattle or pulley bearing type noise. It is not a constant noise and gets loud sometimes. I thought maybe something happened to an accessory on my engine, but using my stethoscope (matco prybar) it is coming from the transmission somewhere. I am sure it is the front pump or something...hell what luck. I didn't touch anything this time! I replaced the filter and fluid and didn't even pull the TC!! Fluid looked clean and the plastic thingy was still in the pan.
If I have to do this again... I will get a properly built 4r70w with shift kit installed and warranty and have the short block done, GT40 heads re-worked some, put in an HO cam and be done. I will pull both out at the same time and drop them both back in.
I would have done this in the first place if I would have known this was going to be a primary vehicle for me!