OK Great news. As I stumbled on in the last post:
I’ve fixed my reading issues, and I’m now reliably reading, in one shot, an entire amiga track from the unmodified standard PC drive!!
When seeing double 1’s earlier, I had the extra second 1 basically thrown out. I didn’t process anything, but just ignored it. Because I assumed I was simply detecting the 1 TWICE, I thought this made sense. However, this detection of back to back ones MUST HAVE BEEN a “10” detected as “11”. I changed the code to write a “10” when it sees a “11” and now it reads every track perfectly!!
This is really an exception issue and if you recall, I was getting like a small percentage of bad bytes. I just re-ran the new track data through the MFMSanityCheck program I wrote and I get 0 bad bytes!! This means everything is perfect MFM!!