Minecraft: Pistons to stop water flow

If you don't mind "cheating", the easiest way would most likely be using MCEdit or WorldEdit. If this building is massive like you say, it would take a very, very long time to move it above ground using pistons. If you really wanted to do this, though, you would put a piston under a block, activate it with a lever, place a block in the new empty space, and repeat. Unfortunately, since you are supposedly underwater, this would be very difficult.

However, I have done testing, and if you were to push a column of blocks up using a piston and one of them is a water source block, the water simply disappears.

Edit: Now that I see you're an admin on a Minecraft server, I'll give you WorldEdit instructions. To use WorldEdit, first install it on your server. Then use the //wand command to give yourself a Wooden Axe. Use this to left-click on the bottom-leftmost block of your building, and right-click on the top-rightmost block. This encloses your building in a "selection". From there, you can //copy and //paste it wherever you please.

The NOT gate also called inverter delays the time exact one tick.

circuit delay: 1 tick

_{from the minecraft gamepedia}

That means the signal on the otherside is one tick to fast. To solve that simply put a repeater in the connection to the other piston.

A repeater also delays the signal with one tick.

When initially placed, a redstone repeater has a delay of 1 redstone tick.

_{from the minecraft gamepedia}

That means your circuit should look like this:

I only have the ability to check that with my eyes and ears and it seems pretty at the same time. Anyway you said you tried that...

Here is your secound answer:

There is a thing called instant inverter. It looks like this:

To get the whole thing working remove your inverter and place this instant inverter at this place. Keep in mind that the piston with the inverter acts strange. But this does not influence the block movememt. Neiter from a normal or sticky piston.

circuit delay: 0 ticks

_{from the minecraft gamepedia}

You find other instant inverter possibilitys in the source link above.