The BANA Chemistry committee has discussed the encircled plus and minus at length and is suggesting that we implement two shorter symbols when the these symbols appear in a spatial diagram. These new symbols have not been published yet, but I see no reason why you can't use them as long as you state in a TN what they are.
For the encircled plus, use "ed" "c" "+" (1246, 14, 346) which is the shape symbol for "circle" followed by a plus sign.
For the encircled minus, use "ed" "c" "-" (1246, 14, 36) which is the shape symbol for "circle" followed by a minus sign.
These symbols are to be used only in the context of a spatial diagram when the plus or minus sign stands alone.
You can move the detached charge symbols in order to accommodate the surrounding material in the spatial diagram, as long as the symbol is close to the letter to which it applies.
Regarding the graph, keying the items is a good idea. Yes, upper-cell numbers are used in a key. I suggest not keying the bottom two formulas though, because they will fit without interfering with the graph line.
"Deprotonation" and "Reaction Progress" will need to be uncontracted. If that doesn't leave you with enough room for the arrows on that line, you can divide "Deprotonation" (deproto -nation). According to Tactile Graphics guidelines, when a label needs to be split between two braille lines, the runover should be left justified, not indented.
Please let me know if you have further questions.