Per your suggestion/find, I checked the vac going to the trans modulator. it said 15hg at idle. I drove it around and at WOT, the vac was around 3-4 hg. It should be close to 0hg as I've read.

So I checked the hg I last recorded about a year ago on the old vac pump and it was 12. I recall that I has a very small thump (not a hard clunk), so I dropped it to 12.5 and now my clunk is not as noticeable. I plan on dropping it down to 12 and then by tiny increments until there is a good balance between optimal shift quality and eliminating the clunk. Because I dropped the vac, the vac is closer to 0hg now.

Note: i am adjusting the vac hg at the blue flying saucer.

i do plan to check the flex disks, etc as suggested above as well. But thanks guys, I believe this solved 90% of the problem.