Ok, so i just got my engine running good, but there is still a knocking type noise. I checked where it was coming from, since i thought it was my exhaust hitting somewhere, but it ended up coming from my tranny, specificly from the space between the torque converter and the tranny. Then we were trying to get it to go away and tried to shift it and we couldnt do that. My car is stuck in nuetral. If any one could explain what the noice was, and why i cant shift i would really appriciate it. Oh yea, i had to replace the shifter linkage, but i was pretty sure i put that on right. ok please someone help

The same thing happened on my buddy's TH350 and it turned out we didn't space the converter correctly and burned the trans pump. It made a knocking noise and then nothing.

I am not saying this is what happened but it could be a possibility.