I just recently pierced a 7 layer aquifer using the double slit method, having never successfully done it before.
I watched, and followed exactly, WanderingKid's youtube video on the matter:
https://www.youtube.com/watch?v=yzdUw92pXH4
. It may help you find a mistake in your method.
In the meantime, let me see if I have this scenario straight.
You started the double slit method. You dug an up-down stair, stepped through it, and inspected the tile it revealed below to reveal it is, again, part of the aquifer. So at least a 2 layer aquifer. Then you started the method. Dug some stairs, built a pump, channeled a bit, began pumping, and went through the entire process for a two layer aquifer. Then, with a relatively dry bottom, you dug into the first non-aquifer layer below and.. it filled to 4/7 water.
Let's assume it was part of the aquifer, and instead it filled up to 7/7. That would mean you did not gauge the size of the aquifer correctly. Part of the double slit method is, when digging down into the last known aquifer layer, to step through using . and inspect the tile below it. For every new layer. Only when it does not show Damp will it be the last layer, though even that is not a sure thing (like running into a vein of ore). Not gauging the aquifer depth would also explain why you are doing the bottom sealing for every level; you think every level is the last when it is not.
The alternate case is if it truly was the last level, the level you dug into was dry, and water poured down from some area above and filled it 4/7 only. In which case it is easy to pump out, though how 4 units of water flowed into the hole in the first place is the real question.