just select the entire map and open texture tool

waterindices has nothing to do with water, it has to do with intersecting geometry
don't worry about ldr leaf ambient, it can exceed 100%

The reason why you have a leak is because func_detail...

Just post the vmf here, some screenshots and the errors here to see if anyone recognizes a problem.

In the mean time try pasting your compile log to interlopers.net/errors and see if it can help...