generally, containments, pathfinding, temperature, weahter, liquid movement, units(population of such region) has to do with FPS
so i would say,
-locking every single animal you do not presently need, like all non-war/hunt dogs, in cage(s)
-only toggle very very few necessary animals available for adoption
-carefully control the population of cats, or other vermin hunter in various mods. basically slaughtering any ecept one or two of the new born cats upon there birth, since there is no sterilization nor abortion in DF. you can change line [BIRTH_ANIMAL:A_D:D_D] in /data/init/announcements.txt into [BIRTH_ANIMAL:A_D:D_D:P:R], thus pause and recenter to the newborn, totally preventing unwanted pet adoption.
-removing containments, esp. blood stained all over your fort and on your filthy dwarfs. there are few ways to do it. first, rain will always clean containments of the tile it lands on n' washs off containments from units, though not every tile gets wet when rain drops fall. also, you can use natural/artificial waterfall or
bath tub like this to wash off bloods etc, then use dfcleanmap to remove them -- i only use this when i'm desperate to get rid of those containments, for this utility is somewhat a cheat
-turn off weather and/or temperature, esp. in area with large body of water that would thaw in warm months and freeze in colder ones. i usually have the game freezed for minutes to unfreeze the ice. yes i love two or more (major) rivers joining together with waterfalls in Victoria Falls' manner.
-embark somewhere with fewer water tiles as possible. aquifer is fun, useful and
fun. also embark with a smaller region.
-buther unwanted animal --- you dont always need 30 cows, bulls and other dozens of caputured elephants, turn them into something does not hold off your FPS! make a reverse cage trap for siegers to enjoy, that once triggered, would release dozens frenzied battle elephants and dozens other meaty excess targets!
-lower population cap in d_init.txt to something like 120 or 150. monarch guaranteed, FPS partially increased.
-the last and least viable solution: BUY A BETTER COMPUTER!