[Ann Bens]

I would uninstall CS5 first run Cleanscript and then install 5.5.

[Ann Bens]

Neither. Both will cost you quality.
Allways use optical zoom and dont scale up in Premiere or AE.
You can use scale if you drop HD footage in a SD project.
But best is to film HD, edit HD and export to SD.

[Ann Bens]

Just set the size to 4.7 gb that is what a single layer dvd is.
If you outputted from Premiere lower your target bitrate of the mpeg2-dvd file a bit to get it to fit. Or use a bitrate calculator.
Did you use Dynamic Link?

[Ann Bens]

That is the way its designed.
Premiere does not reconize the subfolders.
You can place your assets in bins in the Project Window.

[Ann Bens]

Set the export frame rate the same as your footage.
Default is set to 24 frames.

[Ann Bens]

AE’s Remove Grain does a fine job.
I like RE:DE-noise (same guys from Twixtor).

[Ann Bens]

In CS5.5 with a new project with the same clips fresly imported (not the CS3 project) do they still give you issues?

[Ann Bens]

Reinstall windows did you try that?

[Ann Bens]

If your sequence is 1920×1080 make your still 1920×1080 in e.g. Photoshop.
If your sequence is 720×576 make your still 1050×576 with square pixels.

[Ann Bens]

I think you are stuck with the given framerates in the desktop.
But you could try dragging a clip into the New Item icon and see what happens.