If money and develoment time were no object......
5.200" bore spacing, billet blocks, apply the most common bore/stroke combination in use today, single overhead cam design (like the Ford 427 Cammer and the modern-day 4.6L engines), two-valves per cylinder (with a strict intake valve size restriction of 2.25"), modular block design (removable inner-sleeve banks, removable pan/main rail, etc.), "spin-through" valve-to-piston orientation so if the valvetrain stops the pistons can't hit open valves, ability to remove cylinder heads without removing the intake manifold, in-deck 18 head bolt pattern, modular camshaft/rocker carriers, use current combustion chamber design, and...........could go on for days. But the internal designs would all be spec per rules limitations to keep C/R at 6:1.
Fuel system side...take a page from modern electronic engine management of diesel and now gasoline engines and use LARGE electrically controlled direct combustion chamber injectors. 8 large electromagnet nozzles that deliver the fuel at the 12 o'clock location in the chambers. Use the "common rail" design where fuel is pumped into an internal galley in each clyinder head. You'd need an electricity source to fire these big squirters...something in the 24-36 volt range. Have a common "spec" digital management processor that would control fuel and timing maps. Allow the systems to possess a certain amount of closed-loop operation to adjust for "cold" EGT readings...no more dropped cylinders. Also engineer safety functions to cut all fuel flow when crankshaft and/or camshaft accelleration slows dramatically in the event of mechnical failure...no more firebombs.
External crank-driven superchargers would need to remain in place. It's easier to mandate pulley size and teeth number than wastegate or blow-off-valve settings with turbos. Although...centrifugal blowers might be an interesting excersize.
Late night thoughts and musings.