Guessing here Amy,but my guess isn't that your waste pipe is cracked or anything,I would say either the toilet came alil loose from resting on the rotted floor over time and the rocking may have made your wax ring go bad there fore causeing a small leak at times.That is very common.
If your drain is PVC it could be cracked from the stress of a rotted /rocking floor.If it is you should be able to see the crack in the pipe with a flashlite and moving the flange alil.If its a cast steel drain I doubt its cracked or has a hole in it.
As for Tiling the floor,I haven't much expierience at that but do know you need a solid surface so you may need to nail down some I believe its called "Masonite" and lay your grout and tile down to that.
By the way Go Ravens[

]and Good Luck