I happened to set up the scope to trigger on SectorMark and show the incoming stream from the disk heads at various delays afterwards. I noticed that most of the stream was the unmagnetized, essentially erased noise signal but there are patches with strong clock and data modulation.
I then did single shot traces, which would mostly give me noise but sometimes would hit a sector with the good data. Digging through that data showed me that I have a major timing problem with my WriteSector process.
The noise ran for about 240 microseconds then the disk surface had strong clear disk clock transitions. I forwarded almost 35 word times ahead to where it should be writing the sync word and header record, where I found some 1 bits modulated between the clock pulses.
I should be erasing almost immediately after the SectorMark and clock transitions should begin within 2 us afterwards. Something is clearly wrong with my logic, which is all correct from issuing WriteGate/EraseGate onwards but the time that these are first asserted is garbage I guess.
Interestingly, I had very good extraction of the 1 bits and conversely no false bits extracted during the long preamble time where data is always 0 valued. Things are looking up, in an odd way. It does appear that if I can figure out how my WriteSector is malfunctioning and fix it, I should be able to write properly.
Time to go back to my logic analyzer trace of the WriteSector process, but begin the triggering at the rise of SectorMark to give me good timings for when the state machines are transitioning. To do this, I need to change the instrumentation on the fpga to emit those signals.
To reduce the amount of erased junk on the surface, I did a WriteSector of all 12 sectors on cylinder 0 head 0, which I confirmed by running the scope free and watching the signal from the heads. At least I know that the drive is capable of writing clock and data signals.
Working mostly with the scope at first, I triggered on IndexMarker and delayed far enough to be into sector 0. The first 1 bit, for the sync word, seemed to be properly placed inside the sector. Whether the remainder is well formed, correct and in its place will require slow careful examination.