Your probably going to hear this a lot, but that place is small HUGE
Why did you pick such a big embark area?
I wanted to make use of a very large region. This was to be my final fortress in 40d, and I wanted to prove that embark size is not the true cause of bad FPS. For reference, my friend Juice made a 2x2 nanofort recently on similar hardware to mine and got unplayable FPS a short while into construction, whereas mine purrs at 20-33 FPS even in the worst of times, when magma and stone are being moved about. I'm not sure what I have done that keeps the FPS smooth, but I think it has to do with reducing the number of 3D paths around the map (specifically, ramps) to cut down on the geometric complexity of pathfinding. I removed a lot of ramps around the entire map so dwarves would have to take ground level paths instead of goating their way over the mountains.
A couple other tricks, I never export anything except roasts, and I use the most expensive ones I can. I crush anything that's "trash" in a trash compactor so fewer items are around the fort, I dump all the stone on one tile so the game doesn't have to look all over the place when counting and searching for more stones. I also edited the pathfinding weight values in the INI to 1:1:2:5, this can lead to immediate FPS improvements. G_FPS is capped at 20, and game fps at 100.
Anyway, the dwarves work or have worked all around the map, I like to think of it as a theme park with many regions and attractions...