It is not uncommon for the uppers in particular to be darker. The storage method for many I've seen was to coat in cosmoline or other grease and it absorbs into and darkens the wood... Can probably be baked out like on SKS, Yugo Mausers, etc, but have never tried... The uppers are also the rarest component... Under rapid fire and rapid heating, the thin wood has tendency to crack, so my recommendation would be wood upper for display and swap in a beaver barf upper for shooting/range time. Beaver barf being more durable than the beech is why the Czechs made the switch. But your gun and your furniture.
*One of the best methods (insofar as not angering the mrs and also substantially reducing space constraints) I've used is to put cosmoline stocks into a hot attic... Clean off as much as you can w/ paper towels and degreaser, and then wrap liberally with paper towels and put inside a box inside a box and leave it there for a week or so. Ideally, cleaning off what you can each evening and replacing paper towels... For the metal parts, mineral spirits works well. PVC tube for barreled assemblies.