At one point when I owned my TX, it was taking on water as well. It wound up being the thru-hull fitting in the pic below. It actually screws together like a nut & bolt setup. Somehow it came loose and then the 0-ring tore and it was leaking.
One good way to always check for leaks when you're taking on water is to, while on the trailer in your driveway, tip the boat back and fill it up with the garden hose. Be careful not to fill it to the point of covering anything important with water, but fill it up as much as needed and start looking to see if you see a leak anywhere. (water coming OUT)
The back deck of my 95 SLX780 sits right above the waterline with no one on it. I always disliked the fact that water rushes into the footwells when I come in on plane and stop. Dry inside, but always sits low.