Y-axis squaring

How do we align the Y-axis frame? I have the y-carriage on the assembly and need to tighten the nuts on the threaded rods (no vertical plate yet). Using a square and calipers, I'm able to get x-y squared and the carriage moves freely but 1 of the y-corners is off the table surface. The table surface is flat, although not level. I'm thinking the holes in the y-corners are not aligned/square. Would a solution simply be to anchor the 4 corners to a flat plywood base?

That can happen when tightening the nuts. Loosen them, often its on the long rods in the y direction (on a i3), until is sits flat again and carefully tighten them.

Mine sits flat, but i also have it bolted to a piece of plywood. Makes it a bit more sturdy and easy to move.

I had to apply pressure to make all 4 feet flat and at the same time tighten the bolts.

Thanks for your replies.

Even after tightening all the nuts, it is possible to flex the y-axis frame out of plane by picking it up and twisting it with little torque. Attaching it to a flat wood base is ideal -- actually (IMO) should be standard req for all Prusa builds.