For what it's worth (and I imagine everyone has their own technique) - I print a sheet at a time - all the decals at once, if I can. And it's good to print multiples of each because sometimes one layer of water-slide decal isn't opaque enough - you have to double them up to make them dark enough.

After printing them, I spray the entire sheet(s) with just some sort of clear non-water-based spray....I've just used Krylon clear gloss sprays, and that seems to work fine. Maybe 3 coats or so, letting it dry in between coats. This protects it from the water when you're soaking and transferring it.

After you have it on the playfield, I'd try to put some sort of clear over it. You'll have to experiment to see what type of spray and what sheen works on your machine, but I'd guess those water slides aren't going to last very long without something over them. Maybe even clear adhesive mylar discs would work. I like your idea of clearing each insert individually before putting them back in the machine, but I've never done it myself.

I love Old Chicago...it kicks my ass constantly and consistently.

You could try using an eye-dropper with a little 2 pack laquer or suchlike in it and carefully apply to each insert though they would need to be slightly lower than the ( perfectly level) playfield surface or you'd face getting runs in it.