Ah, guess I got the farm plots and greenhouses mixed up then. On the DFMA map the greenhouse POI goes to the giant pit with dropped soil layers, and the farm plots one goes to the bottom-z tiles that were unbucketable.
Generally my rule of thumb is a pile of stone doesn't become unmanageable until it's over 5000 (make the obligatory joke, I'll wait :P) and doesn't become an FPS problem until it's somewhere between 10k ~ 50k. If it's just 'here we have a lot of stone' and it's contained, you can check how much is there by looking at your stocks screen first, then forbidding everything you want dumped in a big sweep and checking again, finding out the difference. It doesn't look like you have any big waterworks or mechanical systems up yet, so you should be fine for boiling so long as you don't have too many masterworks. Just wait until the digging's all done, and in the future try and avoid building out of stone types you know will be boiled later. The number you want for [BOILINGPOINT:] is about 10015u, average indoor temperature. The boiling mist will be a fine breeze.
I've heard adding the [SOIL] tag helps for leaving less stone behind but due to weird biome code doesn't always work. Maybe worth a shot though.
I can't flood my fortress well because the river is too high up. I don't want flooding fun in my fortress just yet.
Two quick ways to get easily accessed water on the bottom floor: One, just dig a big hole and have water pour down. At the bottom use a diagonal access tile as a baffle so it depressurizes and doesn't rise. It won't refill super fast, though, but it's unlikely that's a problem for you. The mildly more complicated way is to dig a big hole and build a pump on the second-highest level drawing from the bottom of the hole. Water will flood the pump, but if mechanically operated from underneath you can seal it off and have fast-filling water pressurized to bottom layer + 1.