Looking good!

With the dot markers, you will find they are plastic so all you need to do is drill through the centre with a 4mm bit then they should pop out with a scribe or even the bit you used to drill.
Then put a drop of super glue in the hole and press your Abalone dots in (assuming they are the same size as the existing ones)

Is your bone nut. PBG one? If so, the string slots will be deep enough. It may look like they are shallow when compared to the stock plastic one but they are cut correctly.
Typically, the low E, A and D strings should sit in the slots with at least 1/2 of the string diameter sitting higher than the top of the nut.
This is to eliminate any chance of 'nut buzz'.

When you instal the nut, the action may be too high.
Check this by stringing up the E srings and if it needs lowering simply sand the bottom of the nut, checking it for hight regulary until you get it to your preferred hight.
Then place a few drops of super glue in the slot and set he nut