If you go to 'The Ultimate BSP Thread' forum topic and find the link on the first post for getting hold of Wally, the texture tool, you can use this tool for creating your PK3 files. Also, if your BSP file is appearing black, have you tried converting your textures to JPG files. Again, you need to modify your .X model to reflect the new image extensions otherwise the textures will not appear when you finally build your BSP file.
Just out of curiosity, why are you using the PVS/BSP tool anyway, it's not very usable and it doesn't even support lightmapping. Why don't you build your BSP with the Zoner BSP compiler tools, also available as a link on the above thread. Also, if you've got Cartography Shop v3, download DreamFlower's .MAP exporter from his site and use the .MAP file to build your BSP using the Zoner build tools. All the info on his .MAP exporter can be found in the Cartography Shop discussion forum.
Personally, If I was you, ditch the PVS/BSP compiler until it is finally updated.