Hello.  So my friend did an engine swap on his 1990 Subaru Legacy.  During the change the shaft came out of the torque converter.  Now, when we start the car there is a clunking kind of noise.  Any suggestions on what can be causing that noise or how to fix it would be so helpful.  Are there any spline alignments in the engine? 

Probably didn't fully seat the input shaft. Often it hangs up 1/4 inch from being fully seated. If the car still moves in gear than that means you haven't destroyed the transmission pump. As for the noise, are the TC bolts tight? 

 

Noise seems to me just about has to TC related. 

Thank you for the feedback John.  I will share this info with him and see if we can't get this noise to stop.  

You also might check to make sure the torque converter is completely seated you have to spin it until you feel it click in 3 times