How about including duplicates of the affected glyphs (with one unencoded and one PUA-encoded slot per glyph)? Would that make everyone happy? Of course the file size would soar. Or maybe two separate font files could be created with clear explanation for the customers. Certainly, this last solution doesn't seem too crisp.
I'm not sure having the bottom curve of the /a tangent to the vertical is what you want. You might want to move the control point to the left to let more light in. Conversely, you can try working with separate shapes for each element of the letter. This way you will have greater control over the pen logic of your design. The idea:
The same goes for /i! The way it looks now it could very well be an uppercase /Idot (the Turkish letter capital i with dot above), only scaled down. The leg width in /R is uneven. The shape of the right spline could follow that of the left spline more closely.