I used the "Embark everywhere" function on successive forts with 7 peasants and no supplies. I wasn't aware that big shots could be gotten from Stonesense - I used the "<" once to get a smaller view then "F2" and "n" to remove the border frame and names. I'd bring the screen in-game up to a level that showed the highest elevation of the entire set of forts that I wanted to encompass with the map then pressed "2" repeatedly until one level below the lowest elevation was showing.
Starting in the Northwest corner, I embarked a fortress covering 2 extra squares around the edge, so I could frame the city with the surrounding countryside and took a screen capture with Stonesense at full screen. I'd port that over to Paint as a bmp image then erase the top and left window frame sections by moving the image up and to the left before resizing it from the bottom and right to erase the bottom and right sections of frame. Once the image was only showing that isometric section, I'd resize the image to 50%, (I tried doing this with the initial image in Stonesense by using the "<" twice, but the resulting picture was much more blurry than using Paint's resize tool), copy/paste that over to the map in progress, (using the eyedropper tool to designate the light blue sky color as a "transparent" background) then scroll the Stonesense map over using trees and building sides as "landmarks" (overlapping trees and building sides helps to ensure that the image has synced in a pixel perfect manner so that no off-section tiling artifacts rear their ugly heads), then repeat the whole process all over again. I'm not sure what happened to that section on the north strip - I was probably just tired and hadn't set the initial height high on the dwarf fortress map enough to make the colors match. That's the kind of off-section artifact thingy I was talking about before, but once I'd started in on the west edge, I remember thinking, "Good enough - I don't want to redo all those fiddly farm bushes again, just leave it." So I did.
Anyway, in order not to have all these wagons and dwarves cluttering up the landscape all over the place, I'd designate them all as "carpenters" and set up a meeting and pen area, plus a 3x3 wood pile down at the bottom of the map, then have them disassemble the cart and tote the wood down there. I did all my mapping on "pause" Once I got to the point where Stonesense showed them again, I re-designated the meeting area/pen and woodpile to the top of the map and waited the few moments while they ported everything up there before hitting "pause" and finishing up that section of the map. The result: no wagons or peasants show up anywhere.
Every once in awhile, a floating window or statue would show up in the sky and I had to erase those and sometimes make the sections certain sizes so that they didn't show up in the final map, which was a bit of a challenge, but other than that, I just repeated the same process about 350-400 times. I would have liked to have less of a smoky pall over all the buildings, but my wife says it gives the picture more "depth", so I guess its a good thing after all.