UPDATE-- **FIXED**
AJP turbo was kind enough to build a test tune for me so I could rule out my tuner's calibration as an issue. After loading his tune, I found the boost oscillation persisted. This led me to believe the problem was mechanical.
I had a feeling that the catch can check valves could be an issue because they are simple spring loaded flaps of rubber vs ball valves. I took the check valves apart and found both to had failed, causing boost leaks!
Next I built a boost leak tester. I found a slit in the driver's side wastegate line under the clamp, where I missed it during inspection of the lines. After fixing this and returning the PVC system to stock until I can get new check valves for the catch can, I took the truck out for a spin.
FIXED!!!! Unbelievable! I think it was coincidence that the boost fluctuation coincided with the downpipe install, or I worsened the wastegate line leak during the install.
So I learned to not forget my roots of tuning DSMs and Subarus and go for a boost leak test right away instead of going down the road of more complicated problems.
Thank you all for brainstorming with me. It's great to have a community like this to learn from.