I noticed on my pwp I have very very small dark specs that seem embedded into the paint on the hood/trunk mostly. Are these just microscopic chips from debris in the air or debris thats actually stuck onto the paint? It's almost like small pieces of sand bonded to the paint in certain areas. I clayed my car today and it seemed to smooth out the surface but didn't remove the spots completely. Is it possible to use too much lubricant while claying? Should there be any resistance at all while sliding the clay over the car?

 

Can't say for sure and I may be wrong. Sounds like IFO or acid rain and you may require using a Decon Kit. I know there are two kits available to the consumer, one is the ABC System and the other is by FK.
Claying will remove imbedded particles from the surface, but will not remove/correct blemishes or surface defects. Too much lube is better than not enough lube - clay is an abrasive and when not used properly can cause hazing or micro-marring. Apply very light pressure and initially you will feel some resistance. After 3-4 swipes, the clay will glide over the area.