Yes. Many mongols were nestorian christians See http://en.wikipedia.org/wiki/Franco-Mongol_alliance
And yes, though they maintained good relations, they had trouble w/ cooperation. I find out also that the Mongols were originally shamanists, a religion common Central Asian nomads, so it won't be wrong to make them pagan. They were also buddhists, not surprisingly since of their closeness to China and Tibet.
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