Acrylics are fine, the "worst" part of them is just that unless you use an acrylics thinner it'll dry with brush strokes, or dab marks from whatever you use for that method. Water doesn't really help bc it just waters it down, while actual acrylics thinner keeps the structure of the paint intact.
I've sprayed my sealant all over the body/face part I've worked on, and it didn't ruin the existing features. You have to be careful when doing so though, since some sealants are aggressive and if you use too much at once, it can make the original paint smear/bleed, and the one you added.
(Honestly, just check for how to apply the sealant before spraying and be careful)
Personally I used Mr.SC since I've only got a few small projects lying around and so it's not that wild to splurge a little, since it's both sealant and base.
No clue, don't think so since it takes allot of time to get a good colour by layering pastels, and it'd probably just result in becoming too heavy/messy look, especially if the original eyes are darker than the colour you want to achieve.
If you state what kinda custom nendoroid project you're doing I think it'd be easier to help, since some people just wanna get the right parts, and then do minor changes to them, while other's do complete art projects with sculpting and adding or removing parts to make their customs.
But for the acrylics:
Get an acrylics thinner, it makes working with acrylics easier and makes it smoother.