I have seen a lot of weird electrical problems in Vanagons and things
are not always as they seem. I once had someone want to sell me an 86 GL
cheap because they thought the engine was bad. They said the oil light
kept coming on at idle and then the engine would slowly die. I went over
to check it out with my oil pressure gauge but never hooked it up. It
turned out to be a shorted alternator that would load down the engine at
idle until the rpms dropped so low that the oil light would flicker.
They did not believe me until I removed the alternator belt and showed
them that the problem went away.

There are not that many parts that would seem able to cause a rpm
specific glitch, both accelerating and decelerating as you seem to say
yours does. Distributor and ECU perhaps. The vibration related loose
connection sounds like the next thing I would hunt for. Do all of the
dash indicators work and indicate properly both before and after the
engine is started?

Mark