Complex sentence: Though the Yuan Dynasty, unlike the western khanates, never converted to Islam, there had been many Muslim foreigners since Kublai Khan and his successors were tolerant of other religions, though Buddhism was the most influential religion within its territory.
Split into simpler sentences: Though the Yuan Dynasty, unlike the western khanates, never converted to Islam, there had been many Muslim residing in Yuan Dynasty territory since Kublai Khan and his successors were tolerant of other religions. Nevertheless, Buddhism was the most influential religion within its territory.