I'm not going to tell you to move things up or down or forward or rearward, I will simply say to go back to the basics and begin your bike setup from scratch.

Start with the saddle tilt, level or slightly nose-up.
Next set the saddle height relative to the pedals.
Next set the fore/aft position of the saddle based on the relative position of your knees over the forward pedal when the pedals are at 3 & 9 o'clock.
Next set the stem height so that you initially have roughly a 90deg bend (varies depending upon who you talk to) in your hips and a comfortable weight on your arms (close to neutral).
Finally adjust the stem length, many ways to measure this but I like the handlebars to block the front axle from my view when I'm in riding position.

http://www.coloradocyclist.com/bikefit

http://www.peterwhitecycles.com/fitting.htm

http://www2.bsn.de/cycling/ergobike.html