The citristrip seems to have done a decent job of removing whatever the clear finish was, but I was interrupted before I was satisfied, and I know there are some spots of it left.
In addition to there being some Citristrip residue you know you need to deal with, it is vital to check there's no finish residue as you refer to later. It seems to be one of the least-mentioned bits of stripping advice but it's a cornerstone of finish removal that one should never expect stripper (even one much stronger/more efficient than Citristrip) to get every trace of finish off in a single application. You might get lucky and one treatment does it, but never expect it (even on pieces where the finish appears to be thin and is in poor condition — worn through in areas, weakened by age, cleaning, light exposure, all of the above.)
I think mineral spirits are usually recommended to clean off strippers
But what do Citristrip's instructions say to use?
As always with generic advice it can be of little help when it comes to specifics. And I know/know of many users who would not use mineral spirits regardless of the stripper used1.
as well as to highlight where some finish might remain
Yup, but actually any clear liquid will do the same — water, isopropanol, vodka (not kidding), denatured alcohol (UK: methylated spirits), xylene or naphtha, acetone or lacquer thinner (UK: cellulose thinners). Someone out there will make use of one of these for this purpose, depending on personal preference and sometimes just what is most conveniently at hand.
but mineral spirits are not for use before a water based stain.
You can use mineral spirits before a waterbased stain, but you will have an easier time if you use something else. In addition to not having to worry about beading, you'll be able to proceed much faster so win-win.
Yes that would have been what I would have suggested you try first anyway since it will probably work well to lift Citristrip residue without being overly toxic, plus it's relatively cheap and widely available.
Once you're sure you've removed all the residue you'll probably need to sand a bit (this is normal) and it would be best to do this fairly uniformly over the entire piece.
And after that I recommend you also wipe down with water. You can do this as a final check for finish residue, but when using a waterbased stain it's advisable to dampen the wood beforehand to pre-raise the grain anyway2.
I don’t want to use it again due to the mess it created
Not that I particularly want to defend Citristrip (I have specific reservations about it, and other similar strippers) but to be fair all stripping is inherently a messy, dirty business. However, if good procedures are adopted3 dealing with the mess can be relatively painless..... at least on flat surfaces, carved work and detailed spindles/turnings are a different story LOL
1 For various reasons, e.g. because of the smell, preferring to use something that evaporates faster, wanting to use something that stands a chance of further dissolving any remaining traces of finish clinging to the wood.
2 You then lightly sand before staining; you're looking to sand off the raised grain only, that's it. Resist the temptation to sand any more than that!
3 Including not letting the stripper dry on the surface, wetting it again if it did dry out anywhere, scraping off the bulk of the sludge and using stiff brushes for inside corners and other tight spots.