Confused setting up bike

I've been riding my Specialized Allez for a few months now and have slowly evolved it into something i feel at home on (well for the most part). The only thing i seem to have trouble with is my handlebar position and my clipless pedals.

Originally i found the bars to low and felt there was alot of my weight going right onto the front. to solve this i flipped the stem over and reversed the angle to make the bars higher.

now i'm feeling that i have to reach excessively far to the hoods which is way beyond comfortable, I ride most of the time with my hands actually about 3 inches further back than the hoods but still on top of the bars and this seems right.

question i'll probably get stick for at some point is it worth changing the stem to something shorter giving me a little more upright position which is comfortable or stick with what i've got to be a little more streamlined?

and secondly does anyone have trouble with the look cleats on their shoes moving even after being tightened?