bore vs stroke
I think for most guys the decision on what your engine geometry should be, should be based on how much RPM, gear, converter are you comfortable with.
If you think 6000 is zinging it up there and you love 3.23 gears, then by all means, put some arm in it.
If you don't mind shifting at 7000ish and you can live with the gearing it takes to do it, the take some 4.10's and throw a 4K converter at it and let it eat.
If you have rocks in your head, and you think 8500 is cool then the biggest bore you can get, a reasonable stroke length (for that RPM 3.79 would be about IT for me) the longest Rod you can stuff in there and get a reasonable ring belt and gear and converter it for it and let 'er rip. But you better have your crap wired tight. The tune up window is almost nonexistent and even a small error is catastrophic...BTDT.
I think for most guys on here, RPM should dictate what you do.