The best thing to do is have a frame that fits your body. Save for that, any modification is going to be a trade off in one way or the other.
Since you are talking about top-tube length, I am assuming the stand over height is okay for you. Fitting a bike for a person with a long or short torso can be difficult (I should know, I am 6'0" with a 30" inseam so I tend to either have too short of a distance between seat and bars, or have issues with stand over clearance.
If you are willing to make the sacrafices, there are a couple things you can do. First, make sure your seat is positioned as far forward as possible. The other thing you can do is continue to play around with the stem and/or bars. A shorter stem is going to help, but you may also want to try a higher stem angle, or even an adjustable stem. I know Giant makes a stem that is adjustable from -10 to +50 degrees. You might look funny with such an upright stem, but apart from getting a different frame, it might work for you.
Remember that moving your seat forward and arms in/up are going to affect the balance of the bike, and perhaps also your pedaling stroke.
If the fit is bearable, but you are still dealing with "numb junk" you can try tipping your seat forward. It may feel akward at first, but it can also improve pressure issues.
Hope that helps.