If the limbs are dead it shouldn't matter when you prune them. I've heard it's generally best to prune live limbs while the tree is dormant, i.e. during the winter and early spring. For what it's worth the forest service usually does pruning during the summer because that's when the manpower is available and the
trees turn out fine. Forest trees aren't orchard trees- they haven't been mollycoddled by centuries of cultivation.
As for the needle layer at the base of the tree: unless it's collecting
water and rotting the bark away where it comes into contact with them, there's no need to remove them. The thickness of the bark is what gives ponderosa its resilience to fire. If there's any large woody debris that will burn for a while at the base of the tree it should be removed, but leaf litter alone will not produce
enough heat to kill all but an already dying ponderosa.