I am "atempting" to change the map art but I could use a mask image of the pathing for the villagers, so I know (mainly with the water) were they begin to swim and such. If this is unattainable, then no problems.

Why not just open the current images, and in a separate layer, paint the paths they seem to walk alot? Keep in mind things like where wet footprints appear. Then just add a layer between the two, and put your changes (or an entirely new map) on that layer. That way you'll have the original map underneath for reference, and the 'common paths' on top.

Keep in mind that they walk straight-line paths until they hit something - they only use more complex pathing if they encounter an obstacle. For this reason, many paths are not natural. (They will not walk toward the edge of a wall, they'll walk right into it, then start to go around.)

Really, the only area where the villagers' paths are not straight is where the farmers come out of the water at the far left of the shore. Sometimes they will hit the cliff near the hive and bounce off to follow the cliff edge round.

Ok, here's what I have thus far; using Illustrator, I've made a vector pathing map of each 16 map areas (MapX0Y0 - MapX3Y3) and included a basic numbered grid. I guess I’ll just let the game run and motion capture it to see when people cross what I think is a barrier and keep track of where that is on my grid system

Sounds like a heap of work.

not that much; each map section is 512x512 so putting a 16x16 pixel grid worked great.