First of all, welcome to the crusade!
to answer your questions:
1)
this set contains pretty much all the paints and basic tools you’ll need for painting Templars and necrons.
You do not need to stick to citadel products for warhammer, their paint line is okay quality and their bundles are nice though
2)
I use these brushes personally, citadel brushes tend to wear out quickly
3)
The starter set I linked above contains clippers as part of the bundle, here is a nice cheap set of modeling tools
The plastic GW uses for its models is fairly malleable so using a file or the blade of clippers would work for removing the markings. Most models do not have these annoying raised markings
4)
My advice for folks just getting into marines with the indomitus box is to buy a redemptor dreadnought as it is a good generalist unit that is tough and strong
The best way to find good units is to look up rules reviews on YouTube for them, most units are decent in a casual setting and the strength of them varies over time as GW tweaks their rules so it’s generally best to go for a variety of units that you like the look and feel of when first getting into the hobby.
Templars are a melee focused army so getting melee units is often a good way to go.
Getting units in a bundle or combat patrol is the best way to get discounts on them
5)
To have the full rules for Templars, you will need the rules for space marines in the space marine codex and the chapter specific rules in this pdf. We are getting a paperback supplement with updated rules at some point in the future though.
6)
I use this glue for my minis, it comes with a brush making it easy to apply
7)
magnetizing units is its own fiddly, awkward process and is usually only done on much larger units such as tanks and imperial knights so they can have interchangeable weapon options, nothing you’re looking at getting really needs any sort of magnetization besides maybe the redemptor dreadnought though that isn’t strictly necessary. here is a tutorial for that if you’re interested.