Update:
I used the latest Marlin and made changes to suite my machine. After a few more changes to direction, stop positions and filament travel, I managed to get it all working nicely and then made a small print.
The first print came out very skewed to one direction, so I made some more changes, reduced the acceleration down a lot, and then made another print. This time it came out fine.

How I got the system working was to first nudge the nozzle down until it opened the micro switch. That would be the zero point as far as the machine is concerned. This is actually below the bed level, so in the firmware I would have to put a positive offset. I raised the nozzle in very small increments until the probing micro switch closed again, checking at each increment to make sure it was either open or closed. When it closed I read the value from the screen and then added 0.3mm for the amount for lift above the bed (this I could experiment with) Altogether I had to lift 0.7mm to get the printing position I needed.
Tried it out and it works. Now I will change the sensing head to a lower pressure design that I have made and test again. No other changes have been made to Marlin to this point, it is all standard code.