Good news indeed!
I’ve managed to create a fully functioning .ADF from a floppy. I matched the output from my hardware/software combination with a “transdisk” output, and it matches exactly.
I used ADFView to extract the files from both, and all files MD5 checksum identically.
ADFOpus still bonks at me saying “root block incorrect checksum”, but no program really seems to care about it. All operations work as they should, with no further errors.
The problem was in fact timing issues with the PC software (Marco’s modified afr.c) and my hardware/firmware. Just sending commands a little too rapidly. I watched the last transfer, and it didn’t hiccup at all.
I’m looking forward to optimizing this thing, but DAMN is transdisk fast. I’ll have a hard time competing.