DSJ13

So I am 5'9' and my inseam is ~31'' using the book method', and I initially bought a Specialized Crosstrail in size M. My LBS had varying opinions on M vs L for me, but I chose the M based on standover clearance. I rode it for a few days but couldnt seem to get comfortable. I went back to my shop and they swapped a longer stem and worked with me which I was hoping would fix it, but with the longer stem I felt like I was still 'on top' of the bars, and lowering the seat would create too much bend in my knee at the 6 oclock pedal.

So, they let me swap it for the large. Trouble with the large is I have virtually no standover clearance. How can I put this other than in plan english? Basically my nuts touch the top tube, but my pelvis still has an inch of clearance or so. So I can lift the bike into my perineum and have the wheel an inch off the ground, but the boys themselves are touching when standing over. Does that make sense?

Anyway I am at a loss here. Stick with the large? Go back to the medium with longer stem? I am right in between sizes. I have an average wingspan. I havent had much seat time on the large yet but right away when I first hopped on at the bike shop the large felt better.