Ok good luck mrmoose hope you get to the bottom of this soon, top marks for trying and persistence!
I would guess the vacuum at idle isn't the problem as it appears to be working properly, and 29inHg at idle verifies that, it's not surprising that it goes down with the snap throttle and returns to 29 without any demands being placed on it.
It is possible that the exhaust outlet (problem 1) connection at where the EGR meets the head is clogged, that would definitely reduce EGR flow, but so would a blanking plate with the 7 mm hole so it's possibly not that. If you say it was almost blocked, there's the possible cause.
Problem 5 the manifold pressure would be low at idle because the turbo has not produced boost until it gets told to
The biggie is the ECU... Maybe someone had a play with it and it's out of specifications. No need to replace, just reflash or tune it, under dyno investigation a good tuner would spot a problem. Replacing it is definitely a last resort.
Cheers Gipsy
although I'm sure somebody will challenge that
even Einstein wasn't certain of his theories.
My 2013 auto D4D DC SR5, prefilter, 3" exhaust and Chip with egt probe, stock SR5 rims with Toyo Open Country AT2 265/65R/17's