Long overdue update, touch-ups with sharpie did not match colors, so I took it off and was able to touch up a bit more in later stages.
Put on 1st coat of Birchwood Casey grain filler & sealer heavy, working into the grain in circular motions. Allowed the first coat to dry 24 hours before 2 thinner, subsequent coats with 4 hours in between them. Last coat was allowed another 24 hours to dry before sanding the whole guitar with 600 grit to prep for tru oil.
The 600 grit did take off some color in places where I may have been a little more heavy-handed. So I touched up those spots using a dobber with the respective dyes at the same mix (glad I measured!). With the color dobbed on, I blended with a clean piece of cheesecloth. This worked really well, and it's unnoticeable where some of the color was sanded off. I also packed dye into the glue spots that I was just going to live with. Pleased that it took up more dye than before, maybe it could grip onto the remaining grain filler? Those spots are still noticable, but much less than before.
At this point, I glued in the neck so that the tru oil could fill the seam where the neck meets the neck pocket. Made sure that the neck was pulled out at the right amount to achieve the correct scale length by first clamping the neck in and measuring, adding a few straight lines with a sharpie across the neck tenon and body in the neck pickup pocket. Pulled the neck out, added glue put back in with the lines straight. Clamped for 24 hours, with one quick grip on the fretboard and body, two more on either side of a Mahoghany 2x2, pressing a block onto the neck tenon in the neck pickup pocket.
With sealant coat sanded back to 600 and dye retouched, started to put on layers of tru oil. With cheesecloth, first layer thick, 24+ hours to cure, with subsequent thinner layers added with no less than 4 hours in between (overnight and life getting in the way allowed a few coats more time than others). Somewhere in between layers I picked up some tack cloth because there was still so much lint sticking from just being in my house. So a few of the deep layers may have some lint...
Currently have the 10th layer applied and cured for 24+ hours. Tonight, will sand back with 1000 grit wetted with tru oil unless band practice gets in the way 🙃 This will ideally create a paste that will fill any remaining grain and contribute to a near-mirror finish I'm looking for.
Aside from finishing, found my issue with unequal space from the low B and high e to fretboard edge to be an unequally slotted nut. The high e slot to edge of the nut was ~3/16in and the low B to edge of the nut was ~1/16in. I've bought a Graphtech TUSQ XL blank in black that is supposed to be shaped for 7-string fanned frets (but not pre-slotted). I'm waiting for in the mail to try my hand at slotting... Can't wait to make one pass of the file too deep and have to go pick up another one. Luckily, If it the one I bought doesn't fit or I do mess it up, I now know that guitar center carries unshaped Graphtech TUSQ XL blanks.