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Your old engine used the flexplate n Crank Position Sensor (CPS). The '89 motor uses the hall effect sensor in the distributor.
You are taking your timing from the wrong place. Your '89 ecu doesn't control the timing like the '90 ecu/ CPS does.
You need the '89 engine, complete '89 ('88 will work too)wiring harness with the hall sensor plug, '89 ECU, '89 MAF, '89 fuel press reg., etc. You may be able to leave the '90 flexplate in and not affect the engine.
Is your turbo a Mitsu or Garrett? If Mitsu; that hose should go to the top of the flame trap. If Garrett; it should go to the blow off valve attached to the head next to the top timing cover on the pass side.
From what you are telling me; it sounds like you are using the wrong timing system.
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