How much of the "old faiths" were still around in the 13th century? Was there "witch hunts" for secret pagans like the Spanish's hunt for secret Muslims/Jews during the (unexpected) Spanish Inquisition?
I unfortunately cannot fully answer this question, but one thing to keep in mind is that "paganism" as a term is somewhat misleading. That suffix "ism" suggests that paganism was similar to modern religions like Christianity and Islam, religions characterized in terms of acceptance of some dogma and by assenting to certain beliefs. Indeed, you even call paganism "old faiths" which recognizes the diversity of the traditions lumped into that label, but which also belies the impression that paganisms were, first and foremost, "faiths". This is, unfortunately, not exactly right.
A distinction worth making here is between orthodoxy and orthopraxy. The former relates to having the right "faith" or the right set of personal beliefs. The latter is related to something like "right conduct"; basically, religion not as a set of beliefs but as a set of practices. Paganism, or at least some forms of it, were generally more concerned with orthopraxy than with orthodoxy.
What I mean to say is this: Traditional religions that we today term paganism were far less concerned with personal faith in a set of beliefs than the modern notion of religion might suggest. Instead, they were dominated by a general sense that to be religious was to be in the right relationship with the gods via the maintenance of traditional practices like sacrifices.
This helps explain the otherwise puzzling charge of atheism leveled against early Christians by the Romans (an example of this charge comes to us from the Apology of Justin the Martyr). The early Christians could be accused of many things, but believing there was no divine was certainly not one of them. The Romans, however, were not just blowing smoke or slandering the Christians. The Christians were atheists in Roman eyes, not because of any set of beliefs, but rather because they failed to uphold traditional religious practices, chiefly sacrifices. To not sacrifice was, in a deep sense, to be irreligious, because Roman "paganism" conceptualized religion primarily in terms of practices, not beliefs.
Anyways, the upshot here is that much of these traditional practices could have survived far longer than you might expect. The traditional pagan festivals or holy sites used for traditional rituals, for instance, could be adapted for new Christian purposes, and often were.
Sorry if this isn't quite what you are looking for, but it struck me that this sort of thing might be interesting