904 causing knocking noise?

Thanks for your help! Plenty of oil and it's circulating. I pulled off the valve cover to see what is going on in there. All is well as far as I can tell. I started pulling wires from plugs. No change on #1 or #6. The sound seems at the rear for sure. The sound changes periodically. Mostly none at idle (except for a randomness to the noise such as in time with engine, and sometimes several seconds with no noise then a random tap here and there. What is the easiest way to check for a problem internally? And... why does it stop when I put in gear (coincedence), or?... Also this filter in the tranny. That might cause it to go in and out of gear?
Thanks for any suggestions or answers.