Its all messed up.

That stem has messed my bike position up.  I had it leftover from last years bike so I put it on the hardtail.  That bike fit perfectly last year but I wanted the cool carbon stem on it.  Its 7deg rise and 100mm long.  Last years stem was 6deg rise and 100mm long.  Using some Sine/Cosine geometry I found that my bars are 2mm higher now because of the stem.  It feels terrible but there is no way I can feel 2mm??  So back to the trusty ritchey stem I go and it instantly feels better. The only other factor I can think is that the Fox fork is longer than the Magura from last year and the combination of the two makes it noticable.

Its crazy how the smallest changes make such a big difference.  I have been battling the position of my cleats on my new shoes as well.  This is all a good lesson of, if its not broke, dont fix it.