According to the readme file that came with my Subsim Super CD, installation goes as follows:
1. clean install of SH2
2. Rename the folder to Pacific Aces
3. Install official 1.1 patch from Ubisoft
4. optional install of Vicker's mod(s) - fireball and/or Oil slick
5. install Subsim 1024 res mod (supposedly already part of the PA package)
6. optional install of Projek Messerwetzer
7. install PA mod, pointing to your Pacific Aces folder
I had the same problems with stuttering sound and TC issues that Red Devil did. Re-installation did not correct the problem.
It got so annoying, I finally deleted PA entirely.