Several years ago I tried to reinstall Combat Flight Simulator 3 and "FirePower," and for some reason half of the planes wouldn't appear no matter what I tried. I had--up until then--no problems with FirePower even through multiple rebuilds of CFS3 due to modding experiments gone awry. After that, I never could get FirePower to work correctly on that computer. All I'm saying is that I sympathize with your plight.
It seems to me that components of your old FS2004 is still somehow affecting the installation process. Perhaps FS2004 is still appearing in the registry? Anyhow, there are some good suggestions in this thread: viewtopic.php?f=25&t=6718
If the registry cleaner doesn't solve the problem, perhaps simply reinstalling FS2004 might. At least you could enjoy the WWII Fighters pack in the iteration of Flight Simulator that the package was actually was built under -- the models on the CD are all optimized for FS2004. The CD was released about the same time as FSX, so the "FSX compatibility" was more or less a bonus.
The first major patch is the 1.2 patch and that should be applied regardless of whether you have installed to FS2004 or FSX. You can find that as a sticky in this forum. After that, if you still can't reinstall to FSX you might be able to manually copy over your models from FS2004 to FSX. There are threads that explain how to do this for some of the other FS2004 products like, for example, the Wings of Power Thunderbolts mega pack.
A2A Simulations waited a few years before creating patches to make the FSX versions of the P-47D, P-51D, Spitfire and Messerschmitt true, native FSX products; the Japanese A6M forever remains an FS2004 port-over. You can find the FSX update patches as stickies in the Wings of Power II forums for each of those four aircraft.
Good luck, I really do hope you can get this sorted out and enjoy the models in FSX.
_________________I like Thunderbolts!
(Link to MySpace tribute page)120th Fighter Wing, Montana Air National Guard