I have just tested my ROM properly in WinUAE by installing OS3.9. Everything went smoothly, and if I cold boot the emulator with no startup-sequence and type "version" it reports kickstart 45.20 and Workbench 45.1 :-)
Setpatch still reboots the machine on cold boot. I'm guessing this is because it's not clever enough to realise it already has 45.20 in ROM, and softkicks the update anyway. Deleting AmigaOS ROM Update stopped this though.
As soon as I get a reply from Willem confirming what hardware I need to programme the chip, I'm going to order :-D
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moto