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From those symptoms, it sounds like something has developed a temperature sensitivity (or perhaps a fan is failing). I'm assuming you had a side panel off the case, when you were testing the power supply replacement. The diagnostic is to see how it does with the side panel(s) off, and perhaps with a small fan blowing on it.
Do you have temperature and/or fan-speed monitoring on your computer? I presume you would have noticed if a case fan was not running at all.
The logical candidates, in no particular order, would be:
Video Card, assuming you're using one.
Memory
CPU or failing CPU fan.
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