Okay. Here are some suggestions. What you do is, of course, up to you.
I marked the rare and very rare glyphs with slashes. Some only occur once or twice. It would not significantly change statistics if they were dropped.
The important ones need to be moved into available slots. The most important ones are EVA-S and the benched gallows. There's enough room for them if you move them to lowercase slots where there are rare glyphs.
I tried to change things as little as possible. This does not shuffle the chart, it's the simplest "fix", and it's not really a fix because they are in slots that may not have anything to do with actual character mappings, but at least you don't lose important parts of the Voynich glyph set.
P.S. FYI, in Voynichese, there are numerous instances of eee, eeee, iii, iiii. These are not scribal errors. The Takahashi transcription does not always record them correctly.
I marked the rare and very rare glyphs with slashes. Some only occur once or twice. It would not significantly change statistics if they were dropped.
The important ones need to be moved into available slots. The most important ones are EVA-S and the benched gallows. There's enough room for them if you move them to lowercase slots where there are rare glyphs.
I tried to change things as little as possible. This does not shuffle the chart, it's the simplest "fix", and it's not really a fix because they are in slots that may not have anything to do with actual character mappings, but at least you don't lose important parts of the Voynich glyph set.
P.S. FYI, in Voynichese, there are numerous instances of eee, eeee, iii, iiii. These are not scribal errors. The Takahashi transcription does not always record them correctly.