From "Jesuit Misionaries in N America, by François Rustang". There are not many comments about clothing. The Jesuits appear much more worried about dying from hunger in the winter, and about being captured/enslaved/tortured/killed by the Iroquois.
a letter from Paul le Jeune, on his first wintering among the natives:
In the beggining I had used one of those eel skins to patch my cloth
cassock, as I had forgotten to bring some patches with me. But when
hunger pressed too hard, I ate them. I assure you that if the whole
cassock had been made of the same stuff, I would have brought it home
much shorter than it was.
So, even in the hardest, first winters, this jesuit was wearing his cassock, and even was supposed to bring patches. He does not say if he would wear anything under or over the cassock. Patching cassocks is
common, I have heard similar "over-patched cassock anecdotes" about various other priests
with limited resources at some point (e.g., St. Josemaria Escriva).
About shoes and canoeing: St Isaac Jogues tells that he was in 6 canoes with French and Huron, when Iroquois come to capture them with 12 canoes. St Jogues decided not to try to flee or hide himself because he did not want to abandon the captured French and Huron. Also, he wonders: "How far could I go without shoes?" And the editor comments that the Indians always removed their shoes when entering their canoeing.
St Jean the Brébeuf on canoe trips with Huron:
Another point to watch is that we do not annoy anyone on the canoe
with our hat. It is better to wear a nightcap. (...) we should not lend
the natives our clothing unless we are willing to do without it the
whole journey. it is much easier to refuse at first than to ask for it
to be returned or exchanged afterwards
Does he mean that large priestly hats would hit and annoy the next Indian in the canoe? I do not know.
St Jogues also comments about how the Indians clothed their slaves and prisoners:
In June, at one intermediate step during the trip to his new master's village:
"At first, Rene and I had been permitted to keep our shirts and trousers (...) the savage who brought me here, regretting the loss of my shirt, was going to send me away completely naked except for a miserable, soiled loincloth."
He begged, and
"Moved by pity, he gave me an old hempen cloth that had been used to wrap the baggage, so that I could cover my shoulders and part of my body".
The hampen cloth hurt him - because the prisoners were
beaten at every stop and he had a bloodied back. When cold weather started they had much cold. The Iroquois did not bother giving them clothes, as they intended to (and did) kill some of them after a few months. In autumn, he was given more clothes by some Indian who pitied him, but they were temporarily claimed back when his benefactor thought that Isaac would be killed, and did not want to lose his lent clothes with his death. He says that his winter cloth (not sure if tunic or blanket) had "seven hands" length
He does not explain if his shirt and trousers were his own (may be he wore them under the cassock? Could he paddle with a cassock?), or if he was given clothes from some dead Frenchmen, or even if he was originally wearing a cassock at all.