The original JD pilot should have just been used for FS2's main campaign. (I'd learned the hard way back in '06 to not use the same pilot for multiple mods >.>) But I started the BP and all of those pilots on a build just before the change to the campaign save system. I think that I have the files from the old system still (backed them up, being the paranoid nutter that I am) would those be helpful?
As far as how far I'd gotten I remember I'd gone and killed the traitorous Unbuntu council member, and the dreamscape after that. The last mission I remember playing was one where you have 6 or 8 different objectives that you have to try to get X amount finished... I think.
But it's been a good 6 months since I last played.
Also, it's looking like all of my pilots' progress was wiped across all mods. But, I've not gotten any more crashes so... yay?