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This is a really fun idea, and I applaud you for having the tenacity to carry it through.
There's a few stratagems that benefit troops that follow a certain god. There's also a separate stratagem that, for one command point, allows you to dedicate an "undivided" unit to a certain god mid-game, to allow access to one of the god specific stratagems. Might I humbly suggest that your army start off "undivided", but if the opportunity exists to use a god-specific stratagem in the game, that you dedicate your unit mid-game (short term this will result in burning extra CPs to get that dedication) instead? So imagine your Raptors have charged into a particularly stubborn unit, and you find yourself wanting to use the "Fury of Khorne" stratagem. Well, you use the "Beseech the Chaos Gods" stratagem first and dedicate them to Khorne. Because they've given in to their bloodlust? At the end of the game if they survive, you could either mark that down as a "point" into the Khorne column (and when the unit gets, say, 5 points for a particular god, they become dedicated to that god), or you could simply decide that they're now dedicated to Khorne?
That way your army is being shaped to the various gods based on how you play - that same unit of Raptors might end up stuck out in the open, and suddenly a Tzeentch Sorcerer has an opportunity to give them a 5+ inv. to protect them through an expected round of shooting. Again, you dedicate the unit to Tzeentch and cast the appropriate power. Thus, that's a point in the Tzeentch column.
Otherwise, you could simply base it on your play style - units that frequently end up bloodied in combat are getting points in the Khorne column, units that wipe our their enemies without any loss in return might be tending to Slaanesh as their arrogance grows. When they ambush and fight from the shadows, they're Tzeentchian. Perhaps those that absorb a lot of damage and make their saves are tending towards the durability that Nurgle is known for?
Either way, if you're willing to go whole hog, as a unit evolves, the scope is there to replace individual models (icon bearers, unit champions) until the unit "evolves" into a unit of Berzerkers, Noise Marines, Plague Marines or Rubric Marines.
Best of luck, be interesting to follow your journey!
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