One thing to check also is there is a coolant restrictor in the heater hoses in by the firewall. It was put in all GT's from 87 or 88 on. But it was put in all cop car Mustangs. Is your car an ex-cop car. If the restrictor is in there maybe it is plugging also. The restrictor should be on the inlet side. High motor speeds were causing heater cores to blow, so Ford put a restrictor in.
How is the heater core? If this is bad or old it could be chunking off into the rad, causing blockage.
Once again buy a thermostat with check ball and try to burp it of air. Air bubbles can be a pain to get out.
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