Thank you all for your suggestions.

Neck is completely flat (checked with a fretboard straight edge). Frets around the 22nd are level. Nut is pretty high but so it the saddle so not an issue here.

Yes, the aftermarket bridge sits lower than the stock. So this could be the main offender.

Photos with the D string installed:

Click image for larger version. 

Name:	IMG_20181231_103052.jpg 
Views:	421 
Size:	220.0 KB 
ID:	29586 I have the saddle as tall it can go.

Click image for larger version. 

Name:	IMG_20181231_103115.jpg 
Views:	406 
Size:	156.6 KB 
ID:	29587 But it is still too close to the fretboard.

I'm keen on the aftermarket bridge so it looks like I will have to deal with the issue at the neck pocket or heel.

I've measured the depth of the pocket and it is around 18.80 +/- .20 mm. Is that the expected depth? If so, I will adjust the neck heel as I feel that is the safest path.

Thoughts?