Games with custom bootsectors? You mean "originals"?
Well, those cannot be converted for emulator use. That's a well known problem.
Try looking around for "crack" versions of your games.
Custom bootsectors should not be the problem,
the problem would be the copy protection
which uses the FDC directly in most cases.
Antiviruses are custom bootsectors and those
copy very well.
(Medway Bootblock for example)
RE: Floppy Archival