In the meantime I have read some scholarly articles, such as this one. Summary: most questions remain unanswered.

I don't claim to be an expert, but I am pretty sure the clef indicates the equivalent of today's F major, the highest note being f'.

This much is clear: the MS was started with lozenge-shaped notes and soon afterwards converted ("updated") to squares.

But there seem to be many erasures whose reasons remain a puzzle. The fourth note of the bar in question has certainly been operated on, but apparently not in the way the article by Ian Pittaway tries to suggest: the original note may have been c' (or g' in Stower's reading), but the upper part of the alleged erasure appears pristine – no trace of an original d' ("a'") whatsoever! Neither lozenge nor square!

All the other erasures remain unexplained as well, unless there is more recent research. If the MS is examined more thoroughly physically, we may get answers to some of our questions. Who knows of such research?