The SOHC engines have a different spacing and bolt pattern of the water outlet flanges off the back of the heads, so the pipe which joins the two heads together and flows towards the water pump of the Pajero 6G72 engine wont bolt up to the GTO motor, same deal with the 3.5 DOHC water pipe, the spacing is different (due to taller block for longer stroke) but the flanges are the same - you could cut slices out of each pipe and re-weld to narrow it down.
You should be able to use a 6G74 DOHC Pajero water pump and thermostat housing, but I'm pretty sure a 6G72 SOHC water pump and thermostat housing wont fit between the wider DOHC heads.
I'm undergoing a similar conversion, 6G72 MIVEC + GTO turbos into RWD Galant-Sapporo coupe -
http://i97.photobucket.com/albums/l230/te71se/Eterna/DSCF1452.jpgas for the inlet manifold, if you rotate the lower intake Y-pipe, you'll be able to sit it like this -
http://i97.photobucket.com/albums/l230/te71se/Eterna/DSCF1473.jpg - therefore not needing to cut and shut the manifold - however that will place the inlet manifold over top the prettier looking of the two rocker covers.
At least you've got your gearbox sorted - that's where I'm stuck haha.
Join up to
http://6g72rwd.forumcircle.com/index.php if you want more RWD 6G72 info. I have some spare GTO 6G72 engine parts if you need.