Well, you can simply edit _ENCODE_3D_MOVIE.avs.
For Half-SBS, you should remove (or comment out) the line with:
StackHorizontal(HorizontalReduceBy2(Left), HorizontalReduceBy2(Right))
and replace it with:
StackHorizontal(left, right).LanczosResize(1280, 720)
The line to replace in Half-T&B mode is something like:
StackVertical(VerticalReduceBy2(Left), VerticalReduceBy2(Right))
and you should replace it with:
StackVertical(left, right).LanczosResize(1280, 720)
In Full-SBS or Full-T&B, the original lines are respectively
StackHorizontal(left, right) and
StackVertical(left, right), and you should replace them with
StackHorizontal(left, right).LanczosResize(2560, 720) or
StackVertical(left, right).LanczosResize(1280, 1440)
Note that I have used the Lanczos resize filter in my examples. You can use another filter if you wish. The basic syntax is always identical: XXXResize(width, height). The available filters are listed
here. Lanczos gives good results but is relatively slow.
I don't think there are other files to modify (except the subtitles, but you don't need them), but I may be wrong.
Good luck!