They also sell flange extension rings to build it up to the floor level. I like to set them maybe an 1/8" above the floor level. Simply set how ever many rings you need on top of the existing flange and use some type of concrete anchor to hold them in place. I caulk the front and sides but leave the back open.

Whenever you caulk around a toilet, you should leave the back open so that if you ever have a leak, it doesn�t leak everywhere. You might need one of those new plastic wax rings. They come with an extra gasket so you can raise or lower the toilet height, this might eliminate the need for the shim.

The crack if there is one might have occurred when the toilet was installed with the incorrect flang (if I am reading this right there was a plumbing redo after the original install?) The larger tile may not be thicker but properly done the installer would have used a larger trowel resulting in a thicker bed of thinset thus raising the toilet. Cranking down on the ceramic is not a good thing especially if it is rocking after the installation.