Gentlemen,
There is little to nothing reliable information available on early mongol warriors. The "pony" story is basically due to Marco Polo and those who based their description on his account. Archeological evidence of early mongol army was scarse, especially since so much was barbarically destroyed after the 1917 revolution in Russia due to the anti-weapon laws.
David Ayalon in his three part work on Mamluks extensively addresses the little information we have on differences and relationship between mamluks and mongols. It seems that earlier mamluks (Baibars) considered themselves to be part of Jelal-al-Din turkoman party that fought against mongols. However after Ayn-Jalat the feelings relax quickly to the point that Qalawun declares in his letter to french king "we and mongols are one nation". He also addresses such issues as language (uighur vs. kipchaq), yasa vs. fiqh and so on.
One should also mention that the depictions of mongol army differ greatly to the point that one must accept that it was composed from very different units of many different people (I remember that Il-Khanid chief commanders at different points were a jew and a nestorian christian, or the story of red haired georgian cavarly from kartlis tzhvoreba), resulting in a rather diverse fighting force. It seems that however their archery was of a different style than that of kipchaqs/mamluks - they used lighter, often biologically "poisoned" arrows and where somewhat more concerned with the rate of fire (even though mamluk standards of aimed fire of 3 arrows per two seconds seem to be rather impressive).
Concerning short stature - it is a rather controversial point. One should address Gorelik's work on mongols and steppe armies for this, but in a short version there is a lot of sources that "noble" steppe people, like "white turks" where of colossal stature
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