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I'm a 40k player starting fantasy, how well could a Skaven army themed around clan Eshin work? What would need to be done to make it work?

don't know how well it would work, but I think it would be really cool to see. Would have plenty of suprise with the assassins....

Also what should I do model-wise, the night runner box doesn't look as good as the rest of the army. Use a lot of greenstuff to give them more covering cloaks, or convert clanrats?

i guess either way could work...
depends on how good you are with greenstuff.... Lol

Few large units of Nightrunners, some gutter runners in fantasy's equivalent of reserve (can't think of the word right now), three assassins (one for each horde of nightrunners, flavour to taste) and a lord with the asf sword, all you need is a bsb and maybe some cannon fodder slaves and your away

Magic being optional

Three units of 15 gutter runners with poison attacks. Assassins are kind of giving away points. Really the best way to use clan eshin is to have the core be standard skaven units but with eshin support. Eshin does really have magic or combat blocks so a whole eshin army would be a problem. But otherwise I think you will like an eshin army, just understand that you will not be able to run into a combat and expect to win but you can harass and target the weaker parts of his army.

Should night runners be thought of as clanrats with throwing stars, or as supporting units to the slave blocks? Or do gutter runner do the job enough that night runners aren't needed for the theme?

Night runners can be useful because they make a 12" move before the battle and so have a little more mobility. But no they can not be seen as clanrats with throwing stars simply because they are so expensive, almost twice as much as clanrats.

If you want theme night runners can be useful, but if you want to be optimal and want to play eshin then gutter runners are the way to go.

The thing about skaven is that they have so many good builds, almost everything in the army book can have a place in any playstyle.