If you're a Luthier you won't have any problems fitting a new tip in. I mainly use the black epoxy because my techniques are (way) less than perfect and the epoxy fills the gaps. The craftsman who built these originally used fish glue and they didn't require any filler of any kind.
If you build guitars, I doubt you will need any either.
Larry Potterfield has a video showing how on YouTube
As far as the checkered panel; don't remove any wood yet. My thought would be to steam it first to try to raise any compressed material for a first step. Then maybe do a little judicious clean up on the checkering at that time if some of the material is really out of place.
If the cracks go all the way through, I would force brown epoxy into the cracks from behind and fortify the bottom of the j-spring pocket with a thin layer of epoxy simultaneously. Be prepared to clean up any excess that squeezes through.
That would also be the ideal time to fill the holes and rough in the checkering. I'm guessing your checkering is 18 lpi. but you need to measure. If it is, I would want an 18lpi double cutter and a single V tool also.
If you really wanted to save the original finish you probably could, but for me, it would be easier to strip and refinish the entire piece cause I'd probably get some scratches fitting the ebony.