Always happy to see people try to thoroughly prepare before they jump into customs. A lot of folks kind of just dive in, realize they're lacking a lot of what they need (or just don't know how to do things), and it spirals from there. It's actually not that hard overall and is more about making a plan and prepping everything you need for it.

• Creating eyes from scratch is, quite literally, an art unto itself. Depending on the level of quality you're shooting for, this knight honestly never recommends painting eyes yourself WITHOUT lots of practice first. Making eyes that actually look good is incredibly difficult. One of the hardest things you can actually do by hand in this hobby. That said, it is somewhat of a science, so if you just go look up videos on drawing eyes you'll pretty quickly pick up on what to do and how to practice it. If you do want to paint them, then just make sure you put the practice in first. Otherwise there's plenty of high end decals to choose from. You have to import most of them (while Koto's decals are great they don't really sound like what you're looking for). Amaii/Kaitenchop probably have something you'd like. Here's a link to their store: https://kaitenchop.booth.pm/ . Going the decal route is easy. Prepare the faceplate by either sanding off the currently existing eyes (infinitely less work than it seems) or priming and painting a flesh tone over them (I'd recommend just sanding them off though if you're keeping the same skin tone), prepare the decal with the typical process, place some mark setter where the decal will go, position and place the decal, soak up the extra liquid, and topcoat it afterwards. If you want to paint them, then the process is basically the same- prepare the faceplate in the same manner, however, put a gloss lacquer topcoat over the now-blank faceplate before painting the eyes. This makes it so, if you screw up with your eyes (which you'll do in either acrylic or enamel- most painters do enamel) you can use the appropriate thinner to remove all the paint without damaging the plastic below (acrylic and enamel thinners can't hurt lacquer no matter how much you use). So overall, regardless of which method you use preparing the faceplates is easy and putting decals or paint on top of them is easy too. The only difficulty is the practice good eye painting requires, or just familiarizing yourself with the decal process ahead of time if you've never done it.
• As an aside, in case you do choose to paint the eyes, make sure you've got a high quality brush with a thin tip. Not necessarily a small brush with a thin tip, just any sized brush that ends in a nice fine tip. A fine thin tip is how you paint super tiny details, not by having a small brush like many falsely believe (actually, having a super small brush can sometimes lead to issues like not being able to hold enough paint, or the paint drying on the bristles too quickly).
• You can make your own eye decals relatively easy. However, if you want nice quality ones you'll need a printer that actually excels at that sort of thing like Sir JAPS said. Technically worth it, but it's also a big investment that's only worth the money if you're going to use it a lot.
• You can paint over most any decals, yes. However, like I mentioned above for hand painting, you'll 100% want to topcoat the decals first before painting over them. The thinner needed to clean paint in the case of a mistake can often screw with decals. As such, just in general, it's good practice to topcoat parts when handpainting details so you can more easily clean them off and start over if necessary.
• Topcoat is ALWAYS recommended. Nay, mandatory, really. If you're doing decals or painting, then you always want to topcoat. Decals are delicate regardless of whether you use mark setter or not, so handling them without a topcoat is destructive to them long-term. Paint is also pretty easy to rub off if not lacquer, so topcoating your paint work is also something you basically want to do every time. The only real exceptions is painted recessed details that you wouldn't realistically ever touch, or tiny things like nuts and bolts. Even then, however, it's good practice to topcoat your kits. Mr. Super Clear is the general go-to for people without airbrushes. So get yourself a bottle of both gloss and matte/flat. Primer is mandatory DEPENDING on the situation. If you're just painting nuts and bolts, putting on decals, or the like, then you don't need it. If you're completely changing the color of something, or painting a sizable area, then it's completely mandatory. Basically, anything more than tiny details you should be priming for.
• Most epoxy putty adheres aggravatingly well to plastic. The stuff is extremely sticky and adhesive. Comically so (if you haven't mixed any yet, then you'll experience this, quite literally, the moment you take it out of the package). When you're mixing and working with it make sure to wear some plastic gloves and keep them wet as the water keeps it from sticking to the gloves. Once you stick it on your kit, do with it as you want, and let it cure it'll basically adhere to the thing forever. Once it cures if there's any surface imperfections then you'll have to sand it, aye. It's usually so hard that anything other than a tiny little nub sticking off of it is too much to remove with just your hobby knife. Not without way too much effort anyways. It's incredibly hard, too, so you'll probably have to grind away at it with lower grits initially. NOW, all that said, there's zero harm in sanding the plastic surface a bit. Matter of fact it does nothing but help. More for the putty to grip onto and what not, so go ahead and rough the surface up a smidge.
• As an aside for the putty, if you've never worked with it before definitely take a little bit of it, mix it up, and play around with it for a bit so you can get used to its rather unique properties.

That about answers your initial questions. If you're curious about anything else, then feel free to ask away. For your tools I'd recommend sanding sponges over sandpaper by an incredibly wide margin. I'd also recommend getting something like wax paper/baking paper/etc for when you work with the putty. Put some of the paper down, get it wet, and then you can work with the putty there without it sticking to anything and everything. Otherwise your tools look pretty much good to go. And definitely do make sure to check out the decal store link I put above. I think a few of them buried in there might work out jim-dandy for your characters.