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The last martin kit I got the inlay dots on the fretboard were already glued in. there was a hump of adhesive of some kind over the dots. It smoothed down fine and looks nice now. I got a new kit with/out inlay. When I glued in the dots from stewmac there are gaps and a little lower than the fretboard. I was thinking, if i had a glue like the one martin uses I would be fine.

Any idea what glue they use? Maybe a super glue gel or something?

martin inlay is even to the fretboard. If the pearl is below the plane of the wood , you can shim the pearl up. You can try CA over the pearl , you have about a 50 50 chance that it will hide the level of the pearl.

You can use either CA (super glue) or epoxy for any inlay. I sand some of the parent wood (ebony or rosewood) and mix a little of the sanding dust into epoxy, put some in the hole or routed channel and push the inlay into the hole. I then put a piece of waxed paper over the inlay and clamp some sort of caul over the top to hold it just flush with the top of the board - the colored epoxy will fill any gaps around the inlay. Scrape it down flush and you should be good to go.

If anyone is interested, the super glue gel worked great. I just applied the glue over the top and clumped it high. Then when it cured level with radius sanding block.