It's called a long rod motor. Essentially what's needed is custom pistons that mount closer to the crown. I've heard of them, not seen them, so can't go into any detail. But it is possible to lose an inch that way. I believe the wrist pin gets tucked in behind the rings - it's that far up.
I hadn't heard or thought of using R65 rods in an R100 engine. Are the crank journals the same diameter? It seems the problem with that solution is the piston would travel an inch farther out of the cylinder towards the crank.
At any rate, there's still the problem of getting the pushrod seals to seal when the cylinder is shortened since they won't align properly. Shorter push rods would be needed as well. Wonder if R65 pushrods woulde work?