Well, I'm a CAD guy and would be willing to put in some hours on this. Sounds interesting, and extremely ambitious as well (both in a good way and a bad way). I'd have to agree with most, in that the best way to get a reliable engine is to use what's already out there, however I'm game to at least give this a try.
One approach I think might be worthwhile is designing something that's over-engineered. Essentially, something bulletproof that will be able to run forever at moderate power levels, but that will also be able to withstand generous upgrading and abuse.
Another approach that appeals to me would be to make a what-if engine. For example, Honda 4-cylinder engines are excellent, but all 4-cylinder engines are inherently unbalanced. What if Honda had decided somewhere along the road to develop an inline 6 (inherently balanced) with the same technology/parts as the Integra Type R B18C engine, or even the S2000's F20C? If they can wring 8k/9k out of those engines, what could a perfectly balanced engine manage? Use their valves, pistons, con rods, injectors, and reverse engineer the cam shafts and crank for 6 cylinders. Oooh, a B27C or F30C would be SWEET. (But long, admittedly.)
Idea the 3rd: take a page from the book of the H1V8
, but bring it down to the level us mere mortals can afford: take 2 common, cheap, reliable, and moderately powerful engines (Honda D series?), take out the parts, and develop a block and crank to make a V8 out of them. The best part about that is the first prototype could be made from a custom crank and two stock blocks strategically cut and precision-welded together. (Hey, Ford did it for the GT90
I'd also be up for the less-ambitious but more useful idea of designing some custom bellhousings to adapt some widely-available engines to a manual transmission. The trick will be picking the transmission/engine combination - I'm going to guess there'll be a lot of opinion to wade through there! (I'll vote for any Honda Civic engine, but I'm clueless on RWD transmissions.)
Either way, count me in for CAD support.