Been there. I knew the exact bike I wanted -- a Y2K Lemond Zurich -- but not the size. I read up on and measured everything and then I bought it at a bike shop that was owned by a someone who had tried out for the Olympics. He measured my inseam and applied a few calculations and concluded my size for the Lemond was 59 cm, not 61 cm. 59 cm was the same size my research indicated, although even a 61 cm seemed small to me, having previously owned 25.5" bikes.

I loved the bike but it took me quite a while to get it dialed in -- almost -- it still was not as good a fit as the 63 cm Bianchi that replaced the Lemond. The Vig took some adjusting too though -- setback seatpost to get the knees in proper positon and a very short stem. Even so, the positon was too aggressive to make the drops very useful, which is a bummer in a headwind.

My latest, a 63 cm Trek Pilot 5.2 works for me right out of the box. Chances are, the reason you are having fit problems is because your upper leg is relatively long compared to your lower leg, which puts you too far away from the hoods when your knees are in proper position. And, your upper leg length will make it difficult to reach the bars without getting stretched out, especially if the bike has a longish top bar like the Lemond.

I wouldn't worry about a lot of exposed seat post except that there is a limit on how much steer tube will be left on most bikes, and with a shorter stem (I retrofitted a 6 cm stem on the Bianchi which was the shortest avail.), you will get less benefit out of the rise on a stem. What you want to look for is if the riding position is too agressive. I like to have the saddle and tops of the bars at the same height.

I'm using the stem that came on the Pilot -- I think it probably is about 13 cm and has a lot of rise -- which makes this the first bike that I feel was actually designed to accommodate my geometry. I've never had a custom bike and I do not feel like I need one now. (I'm 6'3" and the leg length on pants usually says 34").