Lateral multi-layer aquifer digging is pretty straightforward to do, even with huge sections.
Summary: you want the entire edge of the hole through the aquifer layers to be made of stairs, and leave one intact aquifer tile in the bottommost flooded layer so the entire lateral piercing only ever floods in the bottom layer.
The first and most annoying step is to do a standard piercing down to the bottom aquifer layer. Pick any available method. Generally, I do two piercings, one to reach stone and raise magma, and the other to be my eventual gigantic aquifer piercing. (I did this in a hermit game for a single-dwarf-built cannon and in another for a giant vertical surface tree farm.)
Once you are starting with a hole in the ground, the bottom of which is some kind of infinite drain, deconstruct/reconstruct/dig/whatever the edges of it to be stairs. This is probably easiest from the bottom up. The goal is to have every currently layer instantly drain straight down, while still allowing dwarves complete freedom of movement.
Once that's done, you're good to go and dig the whole thing laterally as far as you want. Just designate all z-levels of a particular x,y location to be stairs. You can designate an entire wall at a time, but only one tile laterally at a time. There will be lots of job cancellations, but miners are persistent and re-task quickly.
The bottom layer will always be flooded, unless you do an off-map drain or somesuch, but that's easy, if tedious, to address with magma minecarts.
If you want to obsidian-wall off the entire gigantic piercing, then dig down stairs out one z-level above the outer tiles of the piercing. Construct a track stop that dumps onto one of the tiles, then dump one cart-load of magma at a time until the entire column is obsidian. Repeat, slowly and tediously, around the entire circumference, one column at a time, around the entire piercing. Tell me if you find something less micromanagement-intensive.
To obsidian cast the entire thing, alternate pouring in magma and water. Lots more work than digging it out laterally in the first place.