I understand what you're saying (although I haven't studied engines enough to get very in-depth, I stick to short stroke=high rpm, long stroke=torque).
I would think you need to figure out the exact purpose of the car. Autocross or road track would be a big one. Then build around that. A high RPM screamer would probably be wonderful for a long road track, not as useful on a short turn to turn autocross track. You'd have to have it at high RPM which would make gearing incredibly important, similar to racing a 2-stroke motorcycle.
I, personally, love the planning stages of the build. It's only limited by your imagination and, of course, budget. The better planned out build will always make a guy happier in the end, when everything is perfect! Plan away!!!!
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