So ive tried quite a few things and its very nearly working now.
Firstly something killed the DMA chip, so it now has a nice new IMP DMA fitted instead.
Next up fitted the pullups on the WD1772 and found the 74LS06 also faulty, so that was changed and pullups fitted to that (using good non atari drive)
Removed and fitted floppy header to rule out bad floppy cable.
BTW, the Mega has had the Mandatory fixes done.
This is what happens:
Boot with Tos1.04 and try and format a floppy. It gets all the way to track 80, goes back to 0, then 80, 0 80 and then comes up with an error disk write protect etc. Does this every time.
Boot up with Diag Cart and go to floppy test. Using disk exerciser it formats fine BUT if I use the quick test which formats track 0 and 79 it comes up with a read error and error code F6 IIRC.
Things I've checked:
Metered all tracks from WD1772 to floppy, ls06 and DMA, fixed one but rest are fine.
Scoped out the WD1772 and it behaves as expected as far as I understand at least.
Checked floppy and ls06 waveforms and they are all in sync for WD and RD.
The bit that I don't know is what I should expect the WD1772 , DMA etc to need during the finishing of formatting. I suspect its a problem reading or writing data but I can't work out where at the mo.
Any tips guys?

