Do you own a mityvac? I have been diagnosing my shifting problems with mine and it really helps to see what the vacuum is doing at idle and at ful throttle.
If the vacuum bleed valve on the IP is not working corectly then shifts will always flare theoretically.
Sounds like you've run the gamut of tests though so maybe someone else will have some other ideas.

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'99 S420 - Mommies
'72 280SE 4.5 - looking to breathe life into it
'84 300SD Grey - Sold
'85 300SD Silver - Sold
'78 Ski Nautique