If it can help, here's some tips regarding how i built my fortress.
2x2 map in the d_init.txt was good as i was previously playing 3x3 map but noticed i wasn't even using lots of parts of it, and considering invaders takes so long to come to you, 2x2 is way enough for my forts and fun.
Atom smasher, this one is an absolute considering the huge amount of garbage useless items you'll have on your map with time, regularly going to the z -> Stock menu and press d to dump the many useless things that will accumulate, it really help to keep your item count in check, make sure to have a dump zone ( key i ) in your atom smasher room so the dwarves dump everything there (and if you're using dfhack, learn to love the autodump feature) .
Tons of invaders corpses from various sieges will be useless to your fort (i only kept a few on the corpses stockpile at my village gate for "the atmosphere" ) , atom smashing is always the answer, all those thousands of x X or XX bad clothing or armors too -> atom smash (as current version seems to not allow me anymore to trade them out of my fort).
Quantum stockpiles, again another must have so you don't have giant amount of surface to dig (and lots of dug tiles will create a lot more performance trouble for the pathfinding code) in order to have items stored.
In my fort instead of doing a single quantum stockpile, i decided to do 4 , one for food, one for wood, one for stone and one for everything else just as a matter of preference as i wanted to see what the dwarves were doing, a single one would have been enough honestly.
And make sure every stockpiles part of the quantum does not accept barrel or bin, you don't want to add
bugged stuff regarding container there
Walling sections of the fort that are uneeded, on the bottom of my fort there's the baronness big room, while it does not show (because the retire-unretire hide it again) , there's another big room that extend beyond the east wall (as it was my stone quarry before) that i have walled out, so there is no pathfinding code that will uselessly run there.
Pathfinding performance can be impacted too by the traffic settings, so using d -> o , i setup to Restricted lots of zone that my dwarves have no interest/business to go to but that i didn't want to wall off.
By example the big baroness room, there's part of it that has traffic zones set to restricted (press d -> o to see them) because there's 0 interest for any dwarves to pathfind there.
did the same everywhere else there was no need for the pathfinding code to go.
I have the refuse order to allow gathering outside too ( o -> r -> o ) , simply because if not there will be giant tons of useless stuff lying around after a while, dump them all to atom smash them.
Check when you have body parts or anything else stuck where your dwarves will never go to collect them and mark them to forbid (items in water, items on trees , item on wall top etc...) so when you mass dump things, pathfinding will not try to get them (and fail, but still adding more pathfind calls)
I have used no stairs, only ramps , mostly because i have read that it helps with the pathfinding code apparently, no idea if it is true but as my fort wasn't going to be too complex there was no need of stairs anyways.
I have not dug down to the caverns, mostly because in the end it didn't interested me as out of the rare forgotten beast there's not much fun to have there for me as there's no big invasion armies coming from there, and caverns are usually so convulated that i prefered to avoid having the pathfinding code going nasty down there.