Just a quick update, as I've been able to solve some of these problems with the help of @Mike_da_Spike and @scutters
Font issue in menus fixed (I had multiple fonts in the font folder)
Number of recently added or updated tables increased to 50 using @Mike_da_Spike's program
Topper and Apron screen swapping fixed using @scutterssuggestion about using relative values (had to set apron relative to playfield screen, and topper relative to DMD screen for this to work).
The other issues, I have not been able to solve (changing the order of options in the menu or removing options, losing the aspect ratio of instruction cards on the apron monitor when a table loads, topper video freezing on first game load). Hopefully @Tom Speirs can address these in development. Thanks very much to everyone for their help.