More progress, hoping this kind of info is helpful to someone else eventually.
1. Cam timing. After reviewing the logs, I found the apparent issue: Bank 2 O2s were way off from bank 1 when I had the cams active, but when I disabled them, the O2s leveled out. So, that's not great, but why? Turns out bank 2 had no cam position information at all. This looks like another result of the Elite -> Nexus migration. Hall sensor config got lost in the config. I fixed that in the tune, and will test it again tonight/tomorrow.
2. Tuning. My data here is a little questionable because of the cam timing issues, but it looks like the car is going fat around 2500 RPM and up, in the 40-80 kpa (absolute). I found a corresponding "bump" in the fuel table in that range so I pulled that back down. With the cam issues sorted, and this dialed, I expect the car should start to behave better.
Other issues I found; speedo is a mile off in the tune, it thinks I hit 17,000 kph on my test drive, which I don't think I did. I think this is another "sensor adjustment" issue, combined with the need to re-run the calibration, though the PPM looks right, so that's "odd". The acceleration curve looks right though, so it's reading the reluctor, just scaling (very) wrong.
Outside of that, the car smoked my Chrysler PWM fan controller. Not sure why, perhaps it couldn't take the amp draw? It definitely smoked a FET in it, as now the fan runs 100% when I plug it in. I'm going to move to a different PWM controller, but for now I just plug the module in when I go for a drive, LOL.