ok lotsa questions here:
Yes, leave Assume FPS in there the whole way through when making your jpgs and later. Remember that the whole point of making the fast MJPEGs is they they should be
exactly the same as your AVS file except in picture quality. Same FPS, same resolution, same everything.
I would remove the resize line - you don't need to work in 640x480 and in fact you do not really want to - you can just as easily resize later, and if you ever deside to dump your stuff to DV tape or whatnot you'll have 720x480 to work with.
Which brings me to my next thing: Kill the Crop command. First off you never want to Crop odd numbers unless you're working in RGB, which you're not. In fact you'll notice that if you remove the Bicubic Resize line you actuallyaren't cropping 5 from the other side you're cropping 6 in reality because you can't crop odd #'s of pixels horizontally since you're in YUY2 colorspace (which has half-horizontal-resolution chroma samples).
It's quite easy to crop your final project when you encode it later, and leaving it it 720x480 will 1) speed up the process since there's no Cropping going on, 2) allow you to use the simple 720x480 presets we recommended in the guides.
You can go ahead and crop out black bars later on.
So basically delete the Crop and Resize commands.
However, it looks from your filename like you are using Evangelion as your source footage. Let me tell you something right now: Eva does
not IVTC correctly. The problem is Gainax, in their infinite
fucking wisdom, decided to use a really, really nasty telecining method for their Eva TV masters (which both the R2 and R1 discs are made from). Basically it uses something called "blended frames" where they don't IVTC using the standard 3:2 pulldown method that uses alternating 3:2 fields. Instead the frame switches occur in the middle portion of a field!
Read the DecombHelp.html file that comes with Decomb and go to "Notes on field matching" for an explanation of this phenomenon.
Basically this means your IVTC'd Eva TV will look nasty, especially since the ADV discs were encoded badly anyways. Here's a sample of an uncompressed frame from the AVS I used on my latest XviD encodes of "Just Can't Take It".
http://www.ermacstudios.org/asstastic.bmp
Notice how nasty it looks. That's after IVTC and _three filters_ to clean it up, and it STILL looks like ass.
My recommendation is to obtain the movie discs and use as much footage as you can from them because since they were actually printed on 35mm film, when they make analog masters they make it from the film itself, and don't just copy Gainax's originals. In other words, the movies do not have this problem therefore they IVTC almost perfectly.
As an aside this is one reason you see so much movie footage in my Eva AMVs.
To complete your question, if you do really need to mix TV and Movie footage, my recommendation is to simply crop your TV scenes to widescreen (kill the top and bottom portions) so they match up with the movies. This avoids the Pan&Scan problems of enlarging the movie frames and causing up-resizing artifacts, because there is no Anamorphic disc of the Eva movies (the R2s and the R1s are both 4:3 letterboxed) so you will be losing resolution by upscaling the vertical and horizontal resolution (instead of just the horizontal). See the notes in the guides on "working with anamorphic footage" for an explanation.