if your diaphragm was damaged you should read way-off values on the throttle balance screen in TuneECU - yours around 540 are not bad - and the fuelling would be way off as a result.
if you wanted to test it anyway, you could disconnect it (plug only), also i have a spare i could lend.
have you blanked off that 4th vac line port, the one the cruise control line is connected to? see if it makes any difference?
also did you try disconnecting the idle stepper from throttles and let it idle with the throttle cam against the stop screw.
that'd practically rule out electrical issues and point toward mechanical e.g. vac leak.
also again, might be nothing,, but looking at your pics, the boot appears missing off the coolant temp sensor, wonder is there a prob there, have you checked the coolant temp value in TuneECU looks/behaves "normal"?
(the idle setpoint is dynamic based on coolant temp, e.g. if the ECU sees very cold temps on coolant temp sensor, it will drive the idle revs up.)
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