Glad to hear your on track. So lets go through it.
temperature is necessary for freezing water, interaction between water and magma, evaporation of outdoor pools... It also effects transfer of heat between 2 objects(put magma into a steel barrel, and try to move it with a wooden wheelbarrow.... the wheelbarrow will catch on fire, eventually). generally if the area changes temps across a wide spread from season to season this can cause lag... If temp is off, there is several things that it stops, I prefer temp on.
weather causes the rain, clouds, and a plethora of other things to occur all having to do with weather. Outside pools refill as it rains. It can rain blood, mist clouds can move across the map, evil and poison clouds too.... turning off the weather stops all this from happening... it can cause a huge amount of FPS, especially if you have units moving inside to outside and back, as everything that goes outside in the rain gains dampness and often times they are emotionally affected. Also it has a graphical component that can reduce the fps as it figures when and where to do raindrops and the change in water levels of pools. I prefer it on, but when I hit pop 60+ I turn it off usually.
micromanagement sucks I know.... the problem with workflow is that it doesn't check for resources.... workorder does that but can't be set to an individual shop. the other available option is stockflow, which is even more odd to play with as its based on the stockpile and can be accessed in the stockpile menus. personally I never use stockflow. I use workflow for some things and workorder for other things. if you need something to run once a month... workorder. If its a constantly in use item that resources are readily available all the time, then workflow. If the job needs to know if there is regeants available that are limited or sparse, workorder. Basically kitchen work and farmers workshop are better in workorder. along with complex things such as armor that may need mutiple resources. I use workorder to automate orc raiding. I wish you could save and load workorder settings so that you didn't have to rewrite them every new map.
in comparison workorder requires a lot more hands on approach but the simple fact you can set the conditions to include available regents make it far superior in many ways. I use them both together. some things like filling sandbags is always better for workflow, because its virtually imposible to get workorder to understand sand bag (lol, one of the biggest complaints, workorder doesn't understand difference between box and bag at all, at least in all my experiments with it).
suspended jobs only increase the amount of information in memory, its the unsuspending, resuspending that causes jobs to increase. workflow ticks for jobs not set at shops wont increase FPS as they are handled in a the dfhack program itself.
The primary thing is to reduce routes, the game constantly builds path tables and the more equal distant paths to reach same destination, causes more fps as it has to decide which route to use for each unit. Its hard to explain, but as units move from point a to b the game first designs a path to take from a to b, usually the shortest route, or in the case of multiple equal distant routes it randomly picks one. Then every frame it checks to see if the unit has ran into anything, is it blocked, should it change course, etc. if there is an obstruction (say another unit) it will see if there is another route, and will send the unit that way. if there isn't another route, it will either stop the unit until it can get by, or the unit will try to move past, causing one of the units to dodge, usually with one unit just moving over the top of the other and on their way they go(of course the fun times is a dodge that sends one off a cliff edge for you to later find his corpse in the bottom of a river). this is why hallways should be at least 2 to 3 wide, so that they can just reroute around each other and keep going.... ever watch the guys moving goods to a trade depot or building a roof, when there's only a wall edge to walk on you can actually see this happening, as the number of units with similar routes increase(its also when I lost poor dunderhead as he decided to dodge to the outside instead inside from a wall edge +13z from the ground....). now then so you have all these guys going to these workshops after they are done they have to exit through one of 4 equidistant doors, along 4 equidistant paths to reach 4 identical stockpiles to return along 4 equidistant paths to reach the same workshop to do the next job. it has to make a call about which path to take, and another if its blocked etc....
If your going to be circular make 1 route preferable to the other. You can string say a stockpile A-> workshop A-> stockpile B-> workshop B-> ..... workhop F-> to start. Or you could build workshops that one side enters into say the main fort where housing, dining, temple, tavern is (or a main hall leading to this). The secondary exit is a stair to the stockpile area that is attached to a main hall that exits to where Trade Depot, exterior, paths to mines are. This way there is still circular paths but only one path that is preferred for the workshop to stockpile.
I've even done villages for like kobolds and humans where a shop has a front entrance with a stockpile under, above, around or beside it and no other exit.
Providing shorter routes, does not require multiple routes, that's the key. open spaces aren't bad as long as there isn't too many routes into or out of the space, a 25x25 workfloor so you can run lava under it for furnace operations isn't bad as long as there is only 2~4 exits from the 25x25 space, each exit needs to have its own destination, not a loop back to the same destinations. that's what causes the fps.
When I'm going for authentic, I only make stockpiles for what is needed. If I want to make granite bricks, I make a stockpile for granite stone only usually around the shop, I try to limit its size to 9-16 squares. If I change my mind and want diorite tables, well change the stockpile wants. I've also ran a group of four shops on 1 floor with a stair down to 4 3x3 stockpiles with each one a different desired material. It reduces the crap cluttering the stockpiles, and it keeps only what I can operate on right now near the shop. tie the stockpiles to the shop( I know many hate doing this ). Also stop stockpiling that which doesn't need a stockpile. Things you build into place are better left unstockpiled, such as furniture, trap components, mechanisms, bars, blocks, ammo, coins. If there ends up too much stuff in a shop it will slow the production down... which is a good thing, because if your not using the stuff then you don't need to be building it faster. Weapons, Armor, Tools, stepladders, mugs, etc things your characters walk around with and then drop where they are standing should have a stockpile... There's nothing like hearing that an artifact sword was dropped after the last battle, and some kobold, gnoll, kea picked it up and ran off with it. the only time I use furniture stockpiles is when I'm stockpiling sand bags, and when I'm moving the wagon gear at a new embark to get that anvil inside before a rhesus monkey steals it...damn monkeys.
the reason stockpiles suck fps. if there is an empty square, the game will seek items to TSK to put in the slot. If you make a 5x5 stockpile its going to TSK 25 items to move asap to that stockpile. each TSK is a job which is going to need a unit, you have 20 haulers, they are tested to see which is ready to work, then they go and do the work, they clutter the paths as they move that obsidian boulder from the mines to your stockpile. When I looked through your jobs you had 6 pages of haul item to stockpiles, approximately 240, inactive, looking for a unit. Every time a unit is free the game has to make a call on whether that unit can/will do any of those tasks in the job list. Each additional job adds one more routine to be run every tick looking for someone to do it. this is why sometimes nothing you want gets done, all the units are busy trying to do other jobs. multiply this a few hundred times, and stockpiles can add huge fps.... me I'd rather leave it all at the workshops, and on the ground where its found and send the dwarf that makes the item to go get it... saves having people hauling all together and keeps them available for actual work such as harvesting or moving refuse and food to stockpiles, which are 2 things you must accomplish fast to keep miasma and food waste issues down.
The only things I use minecarts for is to quantum stockpile, move large amounts of stone from a deep quarry to a fortress near the surface, and to move liquids(which MW has too many great ways to accomplish this so I don't use it in MW). The first one I understand you not liking, the second one, well its a hassle but if all of stone X you want is at say z -56 from your base well a 2 point route from the pickup point to the trackstop that dumps it is nice, setup a 3x3 stone stockpile set to the stone you want, lay down a spiral track and have a unit guide it from quarry to dump and push it so it spirals back to the pickup... the main thing is to avoid over usage of stockpiles and utilize them for only what you need to be stocked. Its okay to leave stuff where it sits until you need it.
duplicate workshops doesn't matter a whole lot, if you really need the things they are making.... I usually only have 1 to 2 of any workshop as I don't have a serious need for all the stuff.
stockpile settings should be intuitive, designed once, and good forever, or until you can no longer find the material to fill that stockpile..... I think that's everything you asked about.