Wow, old thread indeed. For future readers - I won't argue for any end of the choices, but for a first-time builder would suggest the typical 393-408's with less clearancing to be done to the block (mostly cylinder bottoms and oil pan rail). Not that it's a biggie, but no sense pushing the edge if you haven't even been in the neighborhood before.
The 393-408's are popular enough to be slightly cheaper as well in similar quality ranges. On the other hand, if you don't mind doing a bit of grinding to your block, and perhaps a few bucks more, for a street engine the 427 is awesome with it's long TDC dwell (timing and combustion efficiency) and quick down-stroke (peak piston velocity) making for sharp throttle response. Of course, if you're using a 6.25" rod in the 427 it has the same ratio as a 6.00" rod 408, so that advantage is lost and maybe we're splitting hairs.
I wouldn't worry about rod ratios too much, as you need to move about .250" to even see anything on the dyno at these power levels. And other short rod ratio issues? Well, if you want your engine to last like one of the millions of Honda Civics with their 1.6L, Jeep I4, or Chev 454's or 400's, then the 427W should last you as well - they are all about the same ratio. Unless it's your daily commuter for the next 10 years, it should outlast you, if you keep it under 6500 RPM or so on the street.
Lastly, I would consider why you want to stroke at all. Okay, that didn't sound right, but get your mind out of the gutter for a moment. Cubes. Right. It's your balancing game, as a 427W only has to turn 6500 to flow at the same VE as a 351W at 7900, with the others falling in-between. Stroking isn't always just about cubes, it can also be about making the same power at lower cost and with more reliable and long-lasting lower RPMs. That's why I built one for my cruiser.
So, I guess I'm saying that each has it's own pros and cons, but they all work. None have negative issues big enough to cause you regret for having chosen that path. The mere fact that the question has caused long-term arguments means the issues are small. Pick your poison and have a blast.