Slight update. Input bearing was fine on the trans.
Turns out one of the 6 adapter bolts backed out and the washer and lock washer were randomly making a ding noise. Had to be my fault I must have missed torquing that one properly as the 5 other ones are fine and there is no way it would come loose seated properly against the lock washer.
But since I yanked the trans anyway I went into "might as well do it now" mode and pulled the front suspension apart to replace bushings. Also found that February of this year, same time I got my swap running, Centerforce came out with a 40lbs flywheel for the 4.0. I just ordered one. PN: 700469 Tick performance has them for $293 shipped. Stock is only 27lbs. I hope this will help with quieting down the counter shaft rattle at idle a little as well as all the other added benefits.
I see photobucket has screwed everyone so when I get time I will fix all the links to pics.