Remember WSD bikes aren't for everyone! Every bike builder uses slightly different geometry so the top tubes from one brand to the next vary widely. I'm 5'3.5" with long legs/short torso. I've never ridden a WSD bike. I shop for short top tubes and don't give a flip about the size of the frame -- I measure the top tube and look for one that will work with an appropriately size stem to maintain the proper handling of the bike. I then make sure the components fit me (adjustable reach levers, proper saddle, proper bars). Stand over height is not the issue for those of us with long legs/short torsos.

You need to take a tape measure with you to the store and actually put it to the frame. Just using a shorter stem isn't always the best alternative as you can sacrifice handling. One of the ways companies say a bike is for women is just having short reach levers and a women's saddle. Well, the shop better be willing to swap the saddle for you or go down the street to the next shop. If you can ride a 58 cm frame you probably don't have reach issues with the levers. Women's shoulders very widely also; I bet a decent LBS can swap out the bars also. A good shop will swap at no cost if they have the same/comparable item in stock or give you credit towards a replacement that fits.

Sore knees can come from test pedals that don't allow you to clip in as usualy, a saddle that is not properly positioned fore/aft, a wide Q-factor, all kinds of things. If you're stretched out over the bike because the top tube is too long you may be pulled forward over the crank.

You've got all kinds of factors to consider but don't get too hung up on a WSD if you can ride something in the 58 cm size range. I highly recommend a professional fit so you can determine the best cockpit length for you and then let the "size" of the bike be secondary. Shouldn't a good LBS credit the cost of the fit towards the purchase of a bike?

PS - You can get an estimate of the total cockpit length by measuring from the ctr of your current bike's seatpost to the center of the stem and also from the ctr of your seatpost to where your hands rest on the bar. This will give you an idea of where to start and if you want to be more stretched out or not.