I think a smoother idle is bit of a ham sandwich - vacuum hoses, plugs, clean injectors, etc. No real mystery meat yet.
The voltage thing has been vexing. I cleaned all the grounds and the junction box, but it still only fires under CSI. Then I setup the dual battery thing just to verify the voltage issue. I removed the starter wire from the junction box and taped it off. So the trunk battery only powered the starter. I added a second battery, common grounding at the cam cover, and +12V to the junction box, hence the fuse 1-5 rail, ignition switch, etc. During cranking, the voltage at the ECU was a steady 12.5V as one may expect. However, no start - ******
I returned everything to standard configuration and jumped the battery from my Toyota like yesterday. But, unlike yesterday, no start!! Then, for grins, I pulled out and cleaned the in-line fuse near the ECU, and wouldn't you know, the car fired up. It's been starting fine all afternoon under its own battery. Let's see what tomorrow brings. (As an aside, if that does amount to the root cause, I may consider replacing it with a blade fuse. I'm slightly allergic to bullet fuses.)
The slave cylinder is fine. I tried starting in gear with the clutch pedal in, but the clutch didn't release. I'll rock it back and forth when my son gets home.
P.S. The fuel pump moans and groans - I'll post a video that may be informative to y'all. It just sounds a little too squealy to my ear. Let me know it's in the zone of "normal".