The round up so far then.
The diagnostic cart seems OK now.
TOS206 won't boot at 50MHz. TOS104 does...
TOS104 & TOS206 will boot and format a floppy fine at 40MHZ, BUT only if "slow TOS" (3XCLK8) delay is used on DTACK.
I can however boot GB6 with "fast-tos" as before.
With "a bit faster TOS" 2xCLK8 delays..
TOS206 formats fine.
TOS104 starts coming up that error box again.
So something craps out with TOS104 for some reason.
Moving for "fast-tos" 3x40mhz clocks..
TOS104 doesn't format.
TOS206 does format.
So, again, it looks like TOS104 has some iffy format routines.
GB6 crashes (4 bombs) on the start of any test, but loads up fine each time oddly.

It will run the GEM WINDOW test, its the only test which doesn't disable interrupts... So disabling interrupts is causing 4 bombs.. which is a problem I didn't have before
EDIT:
Fixed the GB6 crash issue thankfully!
So at least the diag-cart is behaving so at least that is some progress albeit small.