Stock FCDC shocks are 12.6", eye-to-eye. Low Rider shocks are 12". You will be lowering the back a little over half an inch.
Low Rider trees have 1.5 degrees rake built-in. Each degree increase in rake lowers the front end approximately .2", so the front end is about .3" lower on the Low Rider.
Easiest way to make it all even, raise the fork tubes about 1/3" in the triple trees. Support the bike with a jack, loosen the pinch bolts, slowly lower the bike on the jack and allow the tubes to slide up in the trees. Make sure both tubes are raised to the same height. All geometry will be back as it was, just will have a lower bike.