[Yosho]

Side wall measurement is the percentage of the width of the tire.  In other words, it's meaningless to compair sidewall "sizes" without knowing the width of the tire.  You can have a size 40 sidewall that is actually higher than a size 50 sidewall.  

If you've lowered the sidewall height percentage and not increased the width of the tread or increased the wheel size then you're speedo will be off.  

If you've lowered the sidewall height and increased the wheel size but not the tread width... then there is less air volume in your tires and the ride harshness will be correspondingly higher.

In other words, if you're going to fix your problem you'll need to size the tires properly and try to maintain as much air volume as possible.  Low air volume is probably what's causing you that rough ride.