A straightforward way to test the TPS is to use 'T-Pins' which you can get at a local fabric store. You can poke the T-pin between the wire and the seal on the plug for the tps and probe it for voltage at closed, open and then sweep it to make sure it isn't intermittant.
Also to consider, you may want to call the guys at SmallCar up in Tacoma, they do the vanagon conversions (not sure about your '69, is it a wedge or a bay?), and they sell a reluctor wheel that attaches to the CV shaft flange which will give wheel speed to your EJ22 ecu, that may be causing the fluttering as you come to a stop, as it is not seeing the speed of the vehicle still remaining the same as you put the clutch in prior to a stop. This will require that you wire in the wheel speed sensor into the ECU also. That will only effect your 'coming to a stop' symptom though, I would guess.
I would suspect the 'fooler' VSS circuit more than anything, there's not much in the IAC that would cause the ECU to flag a code I would guess. TPS's on the other hand are contact sensors, so they wear out. Not sure if the Haynes or factory manuals have the expected voltage at closed/open throttle, but that's the first place I'd look. I had very similar intermittant nightmares all over the powerband on a vehicle whose TPS had bit the dust.