All of my guitars get a MOP inlay on the headstock (my initials) and some sort of MOP markers on the fretboard. I don't do fancy inlay but I think its an important touch on a hand made guitar. On a few of my fender style guitars I have done inlay with contrasting wood - I just don't feel that bling look correct on a telecaster.
I buy my pearl 0.050 thick and usually precut in the shape I want. I can cut the pearl itself with a little jewelers saw but I find it tedious. Lots of production pearl is cut with cnc's now (and lots of manufactures use cnc's to route the channels for the pearl. I'm also aware of import restrictions on pearl products - everything I use is a byproduct of the shellfish industries and comes with CITES traceability.
I route the channels with the StewMac dremel base as shown in the picture above. It is not a plunge base, I have to do the "plunge" in the middle of the route and work out to the sides. I use a couple of different size bits with I also buy from StewMac because it cheaper (I've heard of people asking their dentists for old burrs that are too dull for teeth but still OK for wood).
I hold the pearl against whatever I'm installing it in, trace around with a fine pencil and try to scribe around it with an Xacto knife. Set the depth of the bit to the thickness of the pearl. When I'm routing a radiused fretboard I put masking tape on the sides to make it flat. Put on my best reading glasses and put a light right down next to the work and have at it.
My channels are never perfect, there are always some little gaps around the edges, so I employ a clever little cheating trick. When I'm ready to actually do the inlay I sand a piece of whatever kind of wood I'm working with and collect some of the dust. I mix that with slow set epoxy and grout the pearl into the wood. The epoxy fills all the voids and is force up along side the pearl. I lay a piece of waxed paper on top and clamp a flat piece of wood over that to try to keep it level. When the epoxy cures I scrape the epoxy off and make everything flat. Pearl sands OK, but scraping will bring back the luster
Here are Gold MOP blocks going into a rosewood fretboard, that is some powdered rose on the sandpaper
View attachment 612256 Same guitar getting ready for Gold initials in the head, the headstock veneer is Spanish cedar so that becomes the grout
View attachment 612257 Here it is in place. Notice that the grout turns out darker than the surrounding wood even tho it is made out of that same stuff. That can be a good thing - it puts a little dark line around the pearl, or it can be a bad thing - it shows off your flaws.
View attachment 612258 There is that guitar with a couple of coats of lacquer
View attachment 612259 When I am inlaying in ebony I usually use ebony dust as above but if you are going to paint it black I might use black epoxy, which is what I suggested to you. I keep some on my bench for drop filling damaged black guitars, its easy to mix a bit and set the pearl. I also thought it would work better for your thin material.
I also have no experience with material that thin so take everything above with a grain of salt. I don't know if its actually inlaid or glued on the surface and the finish built up. I would do a whole lot of practicing before I ever took a bit to my guitar.
Last comment, I have two of those plastic dremel router bases. They only work on dremels that have the big screw on adapter nut on the end. If you would like one PM me a snail mail address and I'll drop it in the mail.