Mike ...will be sending you an email soon.
Been working all weekend and havn't had any chance to properly look at the issues and find some solutions until now.

Nice image by toxic wolf there.

hairydalek...like your approach.

What it can’t do is combine the resulting left/right images into an anaglyph or .MPO file

This does the trick for creating anaglyphs...
http://www.stereoeye.jp/software/index_e.html

But havn't found anything yet that does much .MPO files, except spilt them into a pair. Though thats no biggie as MPO's are usually created in camera.  Theres very also few viewers around. Fuji say use the camera and Sony say buy one of their big tellys.  

Allstereo - thanks for those links.

Pinky - you left the lens cap of your mind on again.