My first thoughts on this is that there is an intercooler coupler not completely connected or something else causing a massive vacuum leak, and that's why you're idling poorly.
Double check everything you removed and worked around for your intercooler install and make sure everything is nice and tight, and if its able to idle listen for hissing or intake noise along the intercooler piping. Also, if you unplugged it, make sure your AFM is still plugged in as that can also cause the symptoms you're having.
For what its worth, I have a 3" turbo back exhaust, Driftmotion 57 trim ct26, upgraded intercooler and hard pipes, and an off brand cone filter (similar mods to what you have). Other than occasionally hitting fuel cut on cold days, I have no problems with my car running or idling. I have no tuning devices, and am running on stock fuel components.
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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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