Three things cause a code 52 (barring the really out there shit): bad sensor(s), bad wires, bad ECU. No the USDM ECU isn't the issue. I suspect the rewire didn't work and needs to be redone. The knock sensors could be shot (even if they were tested) as they're very delicate things and they really aren't all that easy to test (most shops, even Toyota's will tell you to just replace them at this age).
Here's a link to the shielded rewire which solves this problem for most owners:
http://oldschool.supracentral.com/htm/knock.htm