I have some suggestions to this guide:
Tick "Resize", and go with a resolution of 1440X1050. Maintain the aspect ratio and crop.
We recommend this resolution because most S-3D monitors peak at 1680X1050 per eye,
and this is the best fit for a 4:3 image. In the case of 1080P displays (e.g. HDTVs), the
best 4:3 resolution is 1728X1080. Higher resolutions are only required if you plan on
printing 300DPI pictures, or need to blow up smaller portions of the image.
Since 4:3 monitors are rare today I would go for a 16:9 or 16:10 - there are many LCD displays and also projectors which use 16:10 format so I would suggest to resize to 1920*1200 but I would do this in a second step after setting the correct window and eventually crop the image so in the first step I would realign the images without resizing and saving in TIF format (to avoid quality loss) then manually check the stereo window and set it correct and do some cropping (already in 16:10) (save again as TIF) and then in a second conversion step I would do only resizing to 1920*1200 (saving to JPG
For the best results, tick "Only horizontal and vertical alignment
(Don’t use rotation and resize)"
I would not do this since I have seen MPOs with about 2 deg perspective rotation - so please let SPM do all allignments if necessary