Little small new update:
Yesterday in the evening I started with the first calculations for the engine. One quite helpful source was this article from Audi on their V8 Biturbo from Le Mans 1999. AUDI V8 FSI Even if it's a petrol and not a diesel operated engine, there is a few technical information regarding the Audi engine in there.
My research lead me to a stroke/bore ration of a value between 0.94 and 0.98 - a gentle short stroke engine. I've no guarantees that it's right, but it sounds quite usefull. The only available data were from the Audi R10 with a ratio of 0.98. I expected a bit a different ratio for a V6 (Audi R18) engine than for a V12 (Audi R10 -2006).
With the given capacity of 3700ccm distributed on six cylinders and the ratio between 0.94 and 0.98 I got this specifications:
and a length of the complete engine with camshaft drive system of 392mm.
I hope that I'm not completely wrong. It was much easier to calculate the dimensions for the Renault RS27 of the RB7 because the F1 regs dictates you most of the specifications.
My worksheet for the engine. A bit doodle and a comparison between F1 and Le Mans engines. At the top you can see the first cross section of the engine block. The red lines are the silhouette of the rear end of the monocoque.