After fighting with it some more, trying different things, I finally found the problem to the engine not wanting to run after cold start. One of the things I found out a while back was that if I unplugged the MAF connector, the engine does run, but probably in the limp-home mode. So I should have pursued that, as the problem turned out to be a slight distortion of pin 50 on the EEC connector. It seemed that I broke off the little plastic finger that kept the pin in the connector, so that when I plugged the connector onto the EEC, the pin in the connector was pushed to out the back. Yet when I pulled off the EEC, wire tension pushed the pin back in position, so it always LOOKED OK, even when I was doing continuity test. Once I saw the pin in the connector being pushed out, I forced it back in, and magically, the engine cold starts and runs as well as the SD computer did.
Now it seems to have an idle surge when warmed up, where it bounces between 500-800 rpm about 2 times a second. More fun to be had.