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You might want to check out this thread. http://forum.paradoxplaza.com/forum/showthread.php?585705-Experiments-on-how-to-play-as-a-pagan

I certainly can't help you mod it (don't know how mod) however as mentioned in that thread theres cheats to do it.

Within the game I believe if a pagan vassalised you, you have the option to convert. However, I'm unsure of that, as my source is videos on youtube of the beta (someone playing a russian faction became tengriist I believe).
 
I can say that if you start Christian and convert to any kind of paganism, you can continue. If you save, you can reload as yourself, but no other pagan. I'm currently playing a pagan now.
 
I hope if they ever make an expansion for this game it will be playable without cheats. And expansions will come some day I am sure. Big question is just when. I suspect the reason it's not playable is due to quality testing. Developers might have focused on christian rulers due to the (doh!) name of the game, and that muslim game mechanics are not good enough for this launch. Try the cheat and see if your game experience is somewhat weird, or you might prove me wrong. Im only making an assumption. I see no other reason they should close it, since it playable in most of their other games. It would be nice to have this information confirmed by someone though.
 
Can't you just use the demo "exploit" and click on a pagan while the map is zooming in?

I haven't tried that on the full version, not sure if it still works.
 
I can say that if you start Christian and convert to any kind of paganism, you can continue. If you save, you can reload as yourself, but no other pagan. I'm currently playing a pagan now.

Presumably then you could start a game as a random christian character and then immediately save and quit. Then edit the save game to say the 'active' player character is the pagan or muslim you actually want to play with and see if it lets you reload as them instead.
 
Presumably then you could start a game as a random christian character and then immediately save and quit. Then edit the save game to say the 'active' player character is the pagan or muslim you actually want to play with and see if it lets you reload as them instead.
Tried that, didn't work. The only way for now is to use the char-change cheat.
 
This omission is a bit odd since once of the release DLCs adds faces and sprites for Mongol factions...would guess it's a planned future feature. Cheating the system is possible though, enjoying a good game as Lithuania at the moment, interestingly there's also references to the Baltic gods like Perkunas in event texts...
 
It's been confirmed that a Muslim DLC will be out in the foreseeable future, and Paradox hardcoded it so you could only play as Christians so that you wouldn't be able to get the DLC content without paying.
 
Played a good century as Erik the Heathen and his heirs, myself, until one of my (also pagan) vassals overthrew me.

There's a building called warrior cult which gives a huge bonus to troops, but on the other hand, you can't wage holy war as a pagan, so expansion is very slow.