Hawkins - if the p3d texture swap program HAS stopped working (you've gotta give it time, as it does take a long time to load and save) use a hex editing program.
I use XVI32 available
herewhich is freeware.
Or you can use any other hex editor.
All you need to do then is open the p3d, and use the "search" function to find the data/ prefix.
Then, you can find all the different textures that the p3d uses (its time consuming - which is why p3d texture swap is so handy)
edit them, save them into your new folder. Change the "data/" path to "/yourfoldername/"
save and pbo it.