Ah OK, that makes it much easier
First of all, it is possible that you have easily missed that the installer of PA automatically creates a "Pacific Aces" folder, and thus, if you install directly to a folder you have created with all SH2 files inside, the new files will not go to that main folder, but to a newly created subfolder inside it, called "Pacific Aces". To avoid this, when you give the installer the path, check that it really points to the folder you want.
This would explain your CTD, because the PA exe would start correctly through the direct links created at the desktop, but the game would later not find the units it needs because they are outside from the Pacific Aces folder due to the wrong install.
Hope it helps, but if it doesn't, please post here and I'll see to help you step by step until we get it working.