Have you read the Lewis and Clark Journals? They are back in print, and probably available now at your local library. The journals give the most complete and detailed information about the personnel and equipment taken on the exploration. However, individual members also published diaries, often years later.
This is not my area of interest in American History, so I can't help you with sources off-hand. However, a good University Library would be a place to start. We have some members here who have spent years studying the expedition, and members. We know about the contract guns from the Harper's Ferry armory that were used by all the people on the expedition, and we know that one of the two officers had a private rifle of his own, as well, on the trip. Beyond that, little has come to light. I don't recall reading anything about Hunters using different rifles than those supplied by the Government. Mainly, it was the need for uniform ball diameters for all the guns to lessen the weight of all the material taken on the trip that decided what Kind and whether any different type or caliber of gun was going to be allowed along. Remember that most of the river voyage took place in canoes- not boats. The hunters were put ashore to scout ahead, and obtain fresh meat for the expedition daily. They basically walked from St. Louis to the Pacific, and back again, rather than riding on a keelboat.