do you have an Uprev cable to datalog?
i think you're on the right track there. Did you disconnect the throttle bodies from the loom or bump the butterfly at any point? they are incredibly sensitive and i think there must be some sort of keep alive memory in them. They must be sapping a little power when everything's switched off to keep that memory alive. Otherwise i see no other reason why they seem to make the engine run weird after reconnecting WITHOUT performing the 3 relearns i mentioned above.
Did you do the 3 relearns after you fitted the plenum? (gas pedal and throttle rest position, and idle air relearn). the first two must be done on a bone cold engine (coolant temp below 25 deg celsius). the idle relearn has to be done after a decent drive, as long as coolant temp goes over 85*c i think should suffice.
Otherwise i'd suggest cleaning the throttle bodies and the butterfly valves, check condition of the seal between plastic plenum and metal manifold undernearh, and the seals betweem the throttle bodies and the plenum itseld. Do the 3 relearns after all is reassembled. You must use a stopwatch for the idle relearn because it's very sensitive to timing
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