Well first of all, unless you absolutely need murky pools to refill turn off weather in the init if you haven't yet. You can usually get a very nice speed boost from that, and AFAIK the only thing you lose is pools refilling and rain (which helps clean dwarves and the map somewhat).
I've gotten speed increases from butchering (well, actually throwing into a chasm) caged animals. If you have a LOT of war dogs, consider getting rid of them (they are not terribly useful this version anyway). No promises this will help, it was a few versions ago, but it's worth a shot.
If you have large areas where dwarves rarely path (such and uncommonly used workshops, or construction projects where only 2 or 3 masons ever go, and so on) then mark them as restricted traffic areas. If you have areas where dwarves pretty much never go such as totally cleared out mineshafts with no items in them, either mark them as restricted traffic or better yet wall them off. This post has some more info about using traffic zones to improve FPS (and info on WHY it helps, if you're interested) ->
http://www.bay12forums.com/smf/index.php?topic=56041.msg1212099#msg1212099 Destroy excess unnecessary items such as hair, seeds you don't intend to plant, stones you don't intend to build anything with, corpses, low-value goblin junk, and so on. Large amounts of items can slow the game down (especially if you have temperature on)
Speaking of which - try turning temperature off in the FPS. This can easily double your FPS, though it does make alot of the HFS alot less fun so it's a sort of a last resort.
As for the burrows question - well they are really rather buggy right now so I don't recommend them. Theoretically they should help quite alot with the pathfinding though, especially if you set them up good.