the intake that says K&N on the top should be extremely obvious as aftermarket. lol

But if you were saying actual engine parts wise, there isn't anything visible.

Shop is full of it, a new trans won't get rid of that clunk. (in other words, they're trying to get your money) check the CV joints, subframe bushings, LCA's and if all else fails strut mounts, they all can cause clunks. I got the same issue, but mine is a combo of everything. lol