I think extra connectors under the intake manifold is normal, they could be for the different transmission options/abs/etc. I don't immediately recognize those ones in particular.
Were you able to find a different AFM and see if that made any difference? As far as testing the wiring to the sensor, I would get a look at the wiring diagrams and check continuity of each of the AFM wires between each end an make sure there are no breakes or unusually high resistance.
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1989 7MGTE R154 Targa Top White Package w/Blue Interior
Driftmotion 57trim CT26, Upgraded Intercooler, 2.25" Hard Pipes, 3" Turbo Back Exhaust with Test Pipe, HKS VPC w/GM 3 bar MAP sensor, APEXi S-AFC, Walbro 255lph fuel pump, ProSport EVO Series Boost / Fuel Pressure / AFR gauges, Lotek a Pillar Gauge Pod, HKS Type 0 Turbo Timer, Eibach Lowering Springs, Tokico Illumina II TEMS struts, custom powder coated Motegi Racing TrakLite wheels
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