I don't doubt this is doable, but there are a few things that make the
Vanagon job easier.  Vanagon battery does not have to be relocated; the
space where the Porsche oil tank goes is more or less empty.  Additional
headroom the Porsche engine needs is within the bounds of the engine
access lid, so the deck height per se does not have to be raised.  The
Vanagon gearbox is usable with the six; the 66 Micro's reduction boxes
would have to go, which means adapting the Porsche parts to the VW
swing arms.  Perhaps most importantly, the VW brakes would need some 
serious upgrades before you'd want to drive it over 60mph.

Also check the depth of the engine compartment front to rear.  The photos
I've seen of a 6-cylinder breadloaf had the Porsche muffler sitting where
the rear bumper used to be.

Maybe use a 914 transmission and put the six in the middle of the cargo
floor?

Good luck!
B.
Wm Kennedy
kennedy@admin.njit.edu