I bought my bike from Paul Hewitt in Leyland, who stuck me on a simulator and fiddled with various settings etc to decide what size and setup I needed. When I collected it, I felt horribly stretched out (esp having only ridden hybrids before). But as I'd been properly measured, I stuck with it. Now it feels right.
Can't remember how long it took me to get used to the new riding position, but not a vast number of rides.
If you've shortened the stem etc, give it some time before you decide it's still not right (as others have already said!)