With the shorter stem, you probably need to adjust your saddle aft-wards, to redistribute your weight (butt vs. chest) around your changed center of gravity. In my experience, it's rare to change one variable (stem length, stem angle, saddle height, etc.) without having to adjust a second or third. Here's a thoughtful approach you may want to read: http://peterwhitecycles.com/fitting.htm. It may or may not work for you, but ought to at least give you insight into the dynamics of finding your fit.