Solid

Here are a few things I noticed.
blue font = insert
strikethrough = delete

Scott

-------
p.4 Warning message:
"...your entire lexicon will may be ruined."
(The damage may not be serious or it may not affect the "entire" lexicon.)

P.6
"The MDF Legacy Font template is for MDF the hacked font system."
(I'm not sure what this means. "Hacked" font appears again on p.8, where you define it as non-Unicode. I don't think of an off-the-shelf, unaltered legacy font as necessarily being hacked.)

p.7
I think it would be helpful to include "Properties Menu" somewhere in the section heading.

p.7
"For example, if you chose MDF Unicode, select any fields that are not Unicode."

p.7-8
From the dire warning about possibly having the wrong encoding, I would expect to continue directly into instructions for how to avoid that (the Writing System tab). It's a bit confusing to encounter Marker Structure first.

p.16
"Correcting a single entry fixes many may fix multiple errors. " OR
"Correcting a single entry fixes fixed many errors."

p.19-22 Reference section
Parts of this section are redundant with what we've already covered. You could consider moving this section to the start of the Manual, as it gives a nice overview. The other sections seem to give details, so they would be appropriate after the overview.