Well, in any case I don't think the debug log will reveal much. Let me make sure I have the sequence of events correct. You load up the 3.6.9 RC7.9 build, point the launcher's mod command to the PI folder, create a new pilot and start the first mission. During the loading process, it exits out and keeps saying that the tech-add-weapons sexp is pointing towards nonexistent weapon names. Is that right?
I would like to get this working for you, but I don't really have any clue what the problem could be. This type of error message would indicate that it isn't loading the weapons.tbl properly, and therefore that another weapons.tbl somewhere in your FS2 folder is taking higher priority, but I can't see any problems with that in your FS2 install.
See if removing the line "primarylist=pi;" in the PI mod.ini does anything. I can't see why it would if you have renamed the folder as you said, but that's about the only thing I can think of that could be related to the problem.