Some background: In my last fortress, I worked on the plan of digging 3-wide corridors, with rooms allocated in 27x27 blocks. Overall, a plan that worked well, but due to the small distance between the river and the chasm, I could only fit one block in, with smaller rooms either side.
Now, as I dug out the corridors and the 27x27 areas, I allocated the corridors as stone storage. Of course, as the fortress got bigger, I ended up with more stone stockpiles. I continued the plan past the chasm, as the big room areas would be ideal for workshops and storage, laying down stone stockpiles as I went.
Problem 1:
I hit what appeared to be a 'critical mass'. Every three seconds or so, the game would pause, obviously processing something, for about a second. Task Manager showed a usual CPU usage of about 35%, with these pauses corresponding to a 100% usage. I began immediately to switch off various tasks going on to identify the problem.
In the end, it turned out to be the stone stockpiles. I stumbled across it when I unallocated a stockpile in a room area that I wanted to move cloth workshops and stockpiles into. Immediately after unallocating it, although it caused a massive amount of hauling jobs, the slowdowns/pauses disappeared.
In the end, I went around and unallocated every stone stockpile, thinking to hell with being neat.
Problem 2:
After building a bunch of catapults, I needed to get a lot of rock to them so that some peasants set to Siege Operating and nothing else had ammo. So, I created a stone stockpile next to them.
Instead of walking a screen or two east to grab stone (the corridors still had lots of stone in them), all the dwarves proceeded right over to the far east over the chasm, where I was in the process of mining for ore. And as I watched, I saw that the dwarves would stockpile the 'newest' stone. Not the nearest to the stockpile, or the nearest to them when they decide to haul, but the stone that had just been dug.
As a test, I unallocated my massive (and only) ore stockpile, and then dug some more ore out. I then created a new ore stockpile right where the old one was, but covering the empty space that didn't have ore on. And again, the dwarves would haul the 'newest' ore.