Notes

Some context:
I've dig through the surface of the internet in search of all the methods of getting the voice files from both extra and ccc. So far I've been able to get all the ccc files in .wav and at3 of extra (not convertible). CCC poses no problem to me but the at3 of Extra is highly irregular, like it's encoded or something.

Problem:
So here's the deal. I did what I had done to extract files from CCC. Jpcsp would not get me any PGD from Fate/Extra like CCC did. I went to the ISO itself and get a file named data.cpk, then extract it with quickbms. I was happy to get at3 files out of the data.cpk but quickly I found out that they are not recognized even by Sony official programs. My thoughts on this are
1) It is encoded.
2) The files have different header or slight variation than the other at3 files from CCC.
3) It's an older version of at3?

I have no clue and I appreciate any help you can offer. I might be wrong completely so extract it your own way. Maybe you can successfully get something from jpcsp unlike me.
Here's the files:
Extra all at3 - http://www.mediafire.com/download/e6f86yqih7fcoc1/extra.rar
Extra one at3 sample - http://www.mediafire.com/download/xacw4d7cv4t6civ/alc_0109.at3

Languages of forums I searched through:
English
Chinese
Malay/Indon
Japanese
Spanish
Since I couldn't convert them, I turned to finding places to get the already converted files. Only the Chinese have them but I couldn't access to direct downloads the forum unless I have a phone number in China and one of the most popular file sharing site in China is dead (115.com) so lots of links don't work no more. I have someone from who can read Spanish went over the Español sites but got no result. Now I just need someone to find the Russian sites heh..

Programs:
Chances are I already tried all the software you tried. Goldwave was the worst. SonicStage, format factory, sony vegas, sony sound forge, whatever all of them suck ass.

The only ones that worked for me was:
jpcsp (for extracting pgd, you can try ppsspp)
quick bms (intermediate step, converting after extraction)
at3converter on psp (not the celestial being version, for converting again)
Basically a 3 step process
- you extract PGD after getting a clean iso file, meaning you remove the tag of the iso (with ISOTool most likely)
- you convert PGD to at3
- you convert at3 to wav/flac

Hints:
The big picture - http://wiki.vg-resource.com/wiki/Fate/Extra

The super summary for extraction of ccc - http://ngemu.com/threads/ppsspp-at3tool-exe-decoder-tutorial-to-get-music-with-ppsspp-no-longer-needed.156379/

How I extracted fate/extra files - http://proevolutionsoccerphilippines.forumcommunity.net/?t=50279737

Might help (linked comment on youtube) - https://www.youtube.com/watch?v=Xd-l5VAeQfs&lc=z131yvvjlnuufxhzh04chduaxkb0v504pxk0k

Total time I spent to get to what I did: 9 hours straight
Time took to convert all ccc at3: 2 days
Time spent on looking for solutions on Fate/Extra's highly irregular nonconvertible at3 files: 4 days

Notes:
First step is always the hardest and longest.

If after reading this, you still cannot figure out what I said or what to do, I cannot help you. Unless you sound like you know what you are talking about, don't ask me for any help. I've been there. I know there's a solution online.

Please be careful when you install stuff. Also good luck finding ATRAC3.exe and distinguishing the difference between atrac and atrac+. Ahh and you have to find codes for quickbms too if the one they gave you isn't enough (^o^ )

Good luck and godspeed. In other words don't be like me.
Special thanks to Phoenixwings on youtube.