If your files are H.264 wrapped in MOV you are unfortunaly out of luck. CS4 cannot handle them properly. This has been fixed in CS5.
Best is to convert files to something CS4 can handle like Cineform. https://www.cineform.com/neoscene/
You mention proxy files. Sounds good but your final output will still be on the same pc, so nothing gained.
HDV is anamorfic widescreen this means its 4×3 and stretched vertical. To resolve this in AE check the Toggle Pixel Aspect Ratio Correction, sixth button from the right in the comp window.