Options include looking for discoloration on surrounding areas and even putting a paper towel or Kleenex in suspect areas in order to detect a small leak that may not have been sufficient to create noticeable discoloration. Depending on the volume, you may be able to hear dripping in order to help trace the leak. And you may wish to reconsider whether the initial diagnosis was correct or whether the repair was sufficient.
Here are three causes that weren't obvious to us that you may wish to consider:
(1) Around the tub spigot: We had a situation in which we had a leak from a bathroom on the ceiling of the dining room beneath it. We re-caulked the tub and shower surround, did a small test, didn't see any water leaking, and thought we'd taken care of the problem. The next time someone showered the leak reappeared. We eventually figured out that the problem was around the spigot: Water from the shower was hitting the spigot, and because there was not a good seal around the spigot, water was running behind the spigot, down to the floor, and eventually into the dining room below.
(2) The actual copper supply line connections--if you're fortunate enough to have access to them without tearing out the wall: In another house, one with only one floor, we thought we had a leak in our shower pan, but during a remodeling discovered that the hot supply line had not been soldered correctly and water had been squirting out between the wall and eventually out through the brick in the adjoining exterior wall.
(3) Diversion due to insulation: We had another leak that we thought was due to a problem with the flashing between the roof and adjoining siding. After tearing up the roof and the ceiling of the room being damaged, we discovered that the problem a poorly-sealed nail in the roof itself. However, this location was several feet away from where water damage showed up. In this case, the insulation directly below the small leak was sufficient to keep the water from running straight down. Instead it wound around and into another room.
If you had "the sewage line get backed up" all along and didn't do anything to fix it (replacing the water line doesn't) then the sewage line will only get worse.
As for your tub (I think you want me to guess you shower in the tub instead of having both a tub and a separate shower), it probably connects to the sewage line after the clog that affects your toilet.
Best Answer
If the drain is sloped correctly per your local building codes (mine state for drain pipes under 2 inches the slope be 1/4 inch per foot) and it is connected to a stack of the proper size (usually no smaller than 1 1/4 inch pipe) then your drain and trap should operate trouble-free. Also be sure the distance from the trap to the vent or stack is correct (in my county any run over 40 feet will need a larger diameter vent).
As far as running pipe through framing members and joists you must be selective on the location to drill a hole through. This depends one the size of the joist and if it has existing openings already drilled into it. If you plan to use a non-drilled joist one opening (again, depending on the size of the joist)is safe. Be sure not to deviate from the starting slope.