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I'm expanding my search on the KGF for info:
I believe I sealed sanding dust into the mahogany neck grain while grain filling with water based Aqua Coat, but I'm not sure of the root cause of the white grain. Anyone have a similar experience with white grain? I've tried several methods to dye it to hide it with no success. I further sealed it in with three coats of Nitro lacquer.

The advise I've received so far from KGF is to strip it back to bare wood. This is the first guitar I've ever finished so I don't have experience with the pros and cons of stripping it. I have sanded it back, removing a lot of the lacquer, so I could grain seal again with oiled died filler ( no workie). I also tried with straight black dye ( still white grain). What are the pros and cons of stripping the neck to remove the water based Aqua Coat and everything else? Is this the best alternative to begin again? Will stripper strip the water based grain sealer too (desired)? Thanks in advance, and thanks for the feedback I've already received from KGF.

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Measure Twice,

Karl Borum

I just finished a les paul junior clone made out of black limba wood (which is a kind of korina I guess?) anyway this wood had some huge canyons for pores. I wanted it to be a transparent blue, so I dyed the body blue using colorFX dye diluted in water. But I kept getting those white pores too. Some advice I received suggested it was sanding dust pushed into the pores and I needed to do a more thorough cleaning before dyeing. So I stripped it back and tried again making sure to be super thorough with my cleaning the second time, but no dice still the same result. In the end I'm fairly convinced it had to do with the high surface tension of water that prevented the dye soaking into the deep pores. Anyway my solution was a combination of a more thorough pore fill, (I initially wanted an open grain finish but wanted to get rid of the white pores more) and then used a blue toner for my base coat, no more white pores!

Most of the Mahogany I have worked with has natural white deposits in the pores.
I don’t notice it much after finishing.

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wah
Wah-wah-wah-wah
Wah

White grain with clear pore filler can be a thing and the WB stuff is more prone to it. one cause is air at the bottom of the pore. Or it can be sanding debris. Can't see so I do not know which.... but you are where you are.

you have already sanded it back some so I would keep sanding at this point. Are you going to use the same materials again?

Some tips for clear pore fillers;
Do not wipe with solvent when level sanding between coats. This turns the dust to a cement which is initially clear but will dry white. Once this is packed into a pore it is very hard to get out.

Clean after sanding with a shopvac and brush attachment. I also use a 4 inch china bristle paint brush to get any small deposits I see and finally compressed air if I have too. If you use air be sure your supply is absolutely free of oil!!!

Careful inspection between coats is mandatory! Catching problems before they have another coat over them makes the difference between a small delay and starting over.

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Brian

You never know what you are capable of until you actually try.

https://www.howardguitarsdelaware.com/

Thought I would give an update on the Aqua Coat that caused white deposits in the grain of my mahogany neck:
Decided to strip the neck- striped it with 85% methylene chloride stripper, down to bare wood. Slick as a whistle, but with white deposits still deep in the grain. While raising the grain to sand it down, those deposits started to soften and come out. I gently scrubbed the neck with tap water, a toothbrush and a small piece of the edge of a green scotchbrite. The scothchbrite worked best. Just plain ol water softened it enough to pull it out of the grain.

Subsequently, the rosewood body developed some white grain deposits, not nearly as prominent. I cant duplicate what caused it but I will not be using Aqua Coat again - EVER. I refilled the grain with Black Wunderfil product from Rockler Woodworking, shot with vinyl sealer and nitro lacquer and the neck looks sensational. I WILL be using the Wunderfil again....

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Measure Twice,

Karl Borum

Well, I'm glad you are happy where you ended up at least. Can't wait to see it!

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Bryan Bear PMoMC

Take care of your feet, and your feet will take care of you.

I had the same problem with aquacoat on a Wenge guitar I built. Unfortunately it didn’t show up until buffing the final finish, so I also stripped, scrubbed, refilled and refinished....it was great fun. Needless to say the rest of the container went in the trash

Kent