That string alignment looks acceptable to me, but personally I'd not be satisfied with that wonky fretboard edge.
I think it would be worth contacting Adam at PBG and getting his opinion.
re: grain filling - Traditional wisdom and procedure it would be done before staining. However there are more grain filler products available now can be applied after. So now before/after depends on what product you choose.
If you want to use a traditional filler (eg: Timbermate) definitely applied first, and it comes in a black colour (ebony) that will give you the contrast you are looking for.
This is my PBG TLA-1 with ebony Timbermate (Ash body) and water based dye and poly clear coat:
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