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Bassically I have some cadian kraskins and some grey knights. Is it allowed to create a custom squad from this for my space marine army?

Yea, Daemonhunter allies.

I belive your allowed 2 troops, one elite and one heavy or fast.

So yes you could take them as Inquisitorial allies.

if you didn't want to demonhunter allies you could use the cadians as scouts and the grey knights as space marines and make some fluff which makes sense in this. but you would have to make sure it didn't look like just a demonhunter army so people don't get confused

You can always green stuff the models to make em look like marines or just use the "Counts as"