Go back a few years here and find the thread on using a jackscrew to line up the base with the column. There's also a Tormach app note about it, I think. In any case, there are several threads that go into excruciating detail. It may take some digging to find them, but they are in the forum.
Using a level is a good way to start, but it ties you to an external reference. At some point, you start chasing the external zero. This will drive you mad.
Remember: you don't care if the machine is level in an absolute sense to an external reference (the level). You only care that the column is square to the table. You are working with a local coordinate system (machine X Y Z), not one that relates to the rest of the universe. Get the local coordinate system true- X, Y, Z parallel and perpendicular- and if it's tipped 5 degrees to your shop floor, don't worry about it. To put that another way: don't try to zero out two degrees of freedom (machine zero and local gravity field zero) when you only care about one of them.
Switch to a (stiff) long sweep with a sensitive indicator held in the spindle. Tweak the base mounting nuts as needed to get flat while sweeping the table (or a ground flat plate bolted to it).