Figured out the strange CD mounting issue - I'd somehow managed to set the drive to never display on the workbench.
However... I did find numerous issues with the ROMs I'd created (largely a whole bunch of stuff missing), but in so doing, found out how to make a good 1MB ROM pair and also not have to drop the scsi.device from the ROMs at all. New content is as follows:
Main ROM:
exec.library 45.20 (A1200)
1MB_ROM
audio.device 37.10
battclock.resource 39.3
bootmenu 44.7 (68020)
card.resource 40.5
carddisk.resource 40.1
console.device 44.1
cia.resource 39.1
con-handler 40.4 (KingCON-handler)
disk.resource 37.2
dos.library 40.3
expansion.library 40.2 (A1200)
filesystem 45.16
filesystem.resource 45.10
gadtools.library 40.4
graphics.library 40.24 (AGA)
icon.library 46.4.474 (68020)
input.device 50.26 (Poseidon)
gameport_keyboard.device 40.1
keymap.library 40.4
layers.library 40.1
mathffp.library 40.1
mathieeesingbas.library 40.4 (68020)
misc.resource 38.0
potgo.resource 38.0
ramdrive.device 39.35
ramlib 40.2
ram-handler 44.24
romboot 44.3
scsi.device 46.0 (A1200)
shell 45.7
timer.device 39.4
trackdisk.device 40.2
utility.library 40.1 (68020)
version.library 45.5
workbench.task 39.1
NoClick 1.2
RebootFix 1.4
SpeedyIDE 1.1
IDE_DelayFix 1.0 (guess what this does? LOL!)
BPPCFix 1.2
BPPCFix040 1.1
Then in the Extended ROM:
romheader
dummycdstrap 1.0
workbench.library 45.137
intuition.library 40.85
mathtrans.library 100.1
I've tested these to death in WinUAE, so the helpful chap who burnt my last ROMs is going to erase the one's I have and reprogram them for me
Will update again when they're back.