OK - after some twists and turns along the way, I am almost there.
My checkmate a1200 is still utterly in bits over my desk, but is just pending one more part prior to being rebuilt.

So, the TF1260 is now up and running, and thanks to a friend who made me some physical ROMs with the ehide device driver burned in, I am now booting from the TF1260's IDE port, and getting good drive speed (exact speeds depending on the CPU clock).
I sorted my issues with 68060 libraries etc and system seems stable.
I have added heatsinks to the 060 and the 2 CPLDs that get rather warm, and will consider a fan/blower once its all back in the case. I wont really be overclocking too much because as I understand it 75mhz plus causes card corruption on the TF IDE at the minute. Am happy with the ability to run at 62 mhz - its not dissimilar to my SCSI Kit limiting the overclocking on my B1260, and I dont need insane speeds either. Maybe the next firmware update will sort this issue anyway.
All I am now (hopefully) waiting on is a CF adapter with a PCI bracket, that also has a 44 pin 2.5 IDE connector - its currently somewhere between Germany and the UK. This should allow me to run a longer 2.5 cable from the TF IDE to the PCI slot on the back of the checkmate case, so I can access the card externally. Once I have checked that works then I shall reassemble everything.
Work pressures have meant that I have been unable to play much, but hopefully that will ease off soon and I will do some pictures/thoughts on the TF1260 - so far (now its set up properly) it seems to do what I wanted it to, so...result.
Its nice to be able to adjust the clock speed on the fly by a command line (I have some icons setup to adjust the speed currently)