I hope it all goes smoothly for you.
In regard to the manifold, this is the reply I got from Bio240D 2 years ago when I was first thinking about my project.
"I used an exhaust manifold off of a 617 with an adapter plate that blocks off the port for the Fifth cylinder. This is quite easily accomplished. I'm a machinist, so I used a milling machine to make the port openings, but It could be easily done with a die grinder and some patience."
I'm not totally sure what he did but I don;t see why you can't just make some thing that fits into the empty port and then braze it into place. You would want it to bolt the many to something flat so it does not warp. Just an idea though.
There is a photo on this page of Bio240D's engine and some info about thecallaway kit.
http://www.superturbodiesel.com/std/callaway-240d-turbo-article-with-pics-t-456.html
On this page you can see the Rajay turbo kit photos and the angle piece that was used to convert the old style 240D (w115) exhaust manifold to turbo manifold.
Good luck.