I use hide glue and dust when blending or gluing ebony, because it is transparent when it drys, fish glue will work fine as well.
Not a guitar but here is an example, of blending ebony.
This customer wanted a key moved on his Bass Clarinet, the instrument is worth about $16000. Its solid ebony.
Pic 1: The original hole layout
Pic 2: New hole drilled
Pic 3: Old hole plugged with a graft of ebony and perimeter sanded / glued in place using hide glue.
Pic 4: New register pip (brass bit) manufactured and fitted and close up of the new grafted area above it, its pretty invisible to the eye
Steve