paraj pointed out to me that the BPLMODx registers are signed, so with that small change (previously They were treated as unsigned, so adding around 65530 bytes to each line...) and manually adjusting the fetch cycles (since I just want to see how close I am)... I get this (Yes, the disk animation is working too).
Now I need to work out how to do this properly!
-Edit- FYI KS3.1 seems to get stuck in a loop during the booting process at the moment, so it can't boot disks.
-Edit2- Actually more manually mashing in fetch numbers, and it seems it is booting fine, but it is trying to do something weird with the display, so not giving a useful image... My display model is still not quite right...