That looks great! The side grade pattern is really cool with the grain filling.

With the intonation, it looks like you have plenty of travel in the saddles (presuming nothing is too flat) but remember string action at the nut and bridge (and even neck relief to some degree) can effect your overall intonation. Set the intonation last.

I always check the tuning of fretted notes in multiple places (3rd, 5th, 9th) and balance them against what the 12th fret is telling me. It's always a compromise to get the best result from each guitar (sometimes called compensated tuning).