I have a 99 Accord, EX, V6, Auto with 122k. I recently installed a new motor, the result of bad compression on a cylinder, I never did one of these front wheel drive trannies and incorrectly installed the torque converter. I took it to a shop and the ASE certified mechanic properly installed the transmission and now everything is great.

The only issue is now there is an intermittent clunk when the car goes into reverse not right when you first engage the gear rather when you start to roll backward. I am thinking it could be a motor or trans mount issue? I looked at the rear trans mount and it looks at little misaligned in the sense it is about 1/4 to 3/8 to the right as visable from the previous marks on the frame also the circular motor mount on the timing belt side is ripped. I also noticed that front transmission mount has one of the two 14mm nuts fastened that anchored it to the subframe.

Any ideas?

 

Either grab a valve cover & try to shake the engine, or else have someone hold the brake while revving a little bit in gear. Either way, you look for excessive motion at the mounts.