I say get rid of the half-life sdk, you don't need it.
Default wad files that came with the original game can be found in the half-life/valve folder. These wads should never be touched, edited or moved in any way, you only reference these in Hammer/Sledge so you can use the texture that they contain.
When you're mapping for your own mod and you want to use custom textures, place your wad file in the root directory of your mod, like so:
BAD:
..\common\half-life\hrafd\[b]textures\[/b]halfrats.wad
(Only if you wadinclude your custom wad, placing wads in a folder inside your mod root folder will work just fine)
GOOD:
..\common\half-life\[b]hrafd[/b]\halfrats.wad
hrafd is your mod root folder, so that's where your custom wad should go.
Finally make sure that all the wads you're using, both custom and default wads, are correctly referenced in Hammer/Sledge. If you're moving wads around and not update the paths to those wads in Hammer/Sledge, you're potentially going to have problems with textures showing up as purple/black checkerboard textures.
Also note that when you update the paths to the wads in Hammer, Hammer requires a full restart for those changes to take effect.
When you have all these issues sorted out, you can focus on the problems with your map such as the leak and leafnode contents messages.