Try installing the latest AVISynth 2.51 beta from
http://cultact-server.novi.dk/kpo/avisynth/avs_cvs.html. Yes, AVISynth 2.51 should speed up things considerably. Make sure you put an ConvertToYUY2() at the end of your script.
As for saving/loading a project, that actually means saving/loading an .ECL-File from the File menu. In any case, you can always reuse an existing VAF file. Just point at the existing file in CCE but make sure your source hasn't changed dramatically. The CCE manual lists a few cases where you need to recreate the VAF file.