Okay day 3... This has been a little more difficult to complete than I originally started but I'm getting there. After much messing around with my A1200 copying over ADF images and trying to create disks with (what I now know) a faulty drive I have switched to setting up the CF in UAE first.
I'm trying AmigaSYS for now as I see it comes with AmiPro Assembler already installed so I'll see how I go. After running AmigaSYS in an emulator with my A1200 specs I was a little disappointed with the speed but I'm not sure how much is the fact I'm running it on an old MacBook and have the CF hanging off USB - time will tell. BetterWB sounds like a plan B and a good starting place to tinker from.
Signed up for Amibay yesterday so I'll be introducing myself over there soon with the intention of putting my name down for a 8Mb / IDE card if one pops up.
Thank you all.
(found this video helpful for setting up the max transfer rate on the hard drive partitions)
http://www.youtube.com/watch?v=Zd42RsKHm5Y