I haven't used a Wabi, but looking at it online, it's pretty standard geometry. Given your height and long limbs, 55 sounds right to me, too. A friend had a 54cm road bike years ago, fitted to him when he bought it in '97, and he's 5'9" with 'normal' limb length.

The 90mm stem WILL make a difference; you'll be more upright, you may even feel cramped. On the other hand, it may fit you well. Only you will know that.

Just remember this: if you're going to spend ANY significant time on this bike, you need to be HAPPY with the fit; if it's wrong, it won't get better as time goes by. It's not something that can easily be reduced to measurements; it's a "feel" thing, and it just has to feel "right". When all of your contact points (bar, saddle, pedals) seems to "disappear", and just feel like an extension of yourself, you're there.