it all depends on how much power you want to make and how you want to make it. Smaller mains will give less friction but going to the 400 main size does not always mean a stronger crank. thats up to the crank maker.In my opinion, if your buying an aftermarket block, dont get cheap and buy a quality 350 main crank
How much HP are you shooting for on nuts ?
If you want to help the overlap when using the 350 mains, go with a 2.0 dia rod pin.
As was said above, regardless which main size you go with, invest in a quality crank.
The very small difference in size won't due much for overlap and with a 3.750" stroke will do nothing. More benefits to the smaller though, as stated, less bearing speed, friction and heat. My rule of thumb is keep overlap to 2" and under from main journal to stroke. Like Horndog says, you can help some applications going to the smaller rod journal, which in effect does the same thing as the mains and has the same benficial effects. I run 350 mains on just about every small block engine. Only time it will be critical is passing that 2" rule of thumb. The aftermarket blocks also use the same caps for either main, and although the caps are real strong, are stronger when using the smaller diameter main size. The 400 main removes more material from the same cap. Hope this helps.
Oh and x5 on running good cranks, but again the overlap is not that drastic in these, so power and application should tell you what material crank to use, not the overlap in this case.