I've had somewhat similar problems off and on - I don't get numb, but I wonder about too much weight on my hands. As I ride more (and doing yoga), I'm stretching out more and getting more comfortable. One thing that you might observe is where you put your hands on the bars. I used to put the heel of my hand in the "corner" of the bars which is bad because that forces the pressure right on the spot where the nerves run. When I later got a shorter stem, I was more comfortable putting my hands fully on the hoods and that helped a lot.

I think what you're hinting at is whether your frame is the issue. On the one hand, you suggest that you don't have too much weight on the bars, but on the other, a 6 cm stem is exceptionally short, and suggests that you need to compensate for a shorter reach. (I'm guessing that you don't have carpal tunnel problems or you would have mentioned that). The answer is that it's hard to tell from simple measurements. I'm 5'9" and I ride a 52. My wife is 5'5" and rides a 54. One of the issues is that frame sizes are measured based on the seat tube, but the critical measurement is really the top tube length (assuming that you have standover room) since that determines how far your "reach" is.

One of the services that a Serotta fitter may offer is to do a sizing on their "ultimately adjustable" sizecycle. Based on that, they have something called an "X-Y tool" that takes the three critical points in space (bottom bracket, bars, and saddle) that they can then use to compare to stock bikes. I don't know if that was included in your package or not, but I'd definitely ask.

Failing that, I'd check out some new bikes in smaller sizes to see what they feel like.

You could also post some pix here of you on the bike, but that rarely seems to end with a consensus.

Also, as stated previously, road biking is a very different animal from running, and your body will compensate over time.