So what I have done, and what I still need to do. Everything I do needs to be simple enough that I can teach High School kids how to do it. I have several Portenta that students and I have fried.
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I have tested the particle debugger which is a cool drag and drop bootloader.hex file installer, which plugs in nicely to the Portenta with Ethernet Shield which has the JTAG pins cut for a 10 pin connector to fit. The LoRa vision shield does not have the pins cut so only a 20 pin connector will fit. Anyway I have not yet got the Particle debugger working. A small pain point is that Arduino does give the .hex file for the Nano33BLE but not for the Portenta. Theoretically this is not a big issue, but it is frustrating to have to generate the .hex file yourself.
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I have an st-linkv2 but can't seem to get the license and software working.
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I have a segger j-link mini edu debugger, this works with the j-link flash -"lite" installation, so you don't need a license. With a bit of playing around you can install the portenta.bin file to location (0x08000000). So bootloader installation is now not a problem. The orange LED is still an issue on 4 of my Portenta
I will try the first diagram above and see if I can boot the portenta enough to burn a bootloader. It looks like it is just an I2C power connection. I have two breakout boards so will try that. Can anybody think of a way to do the above if you don't have breakout boards? Is there a way to power the Portenta PMIC without an I2C connection?
Thanks to @tjaekel for spending the time on the above diagrams.