So I tore my cs apart.

All the marks look authentic But there is only a big blue ink stamp on the metal shielding on the back side of the pick guard and nothing on the pickups. I have heard of people taking these apart and replacing the insides with junk.

I see alot of custom shop parts for sale and I notice some stuff like pickups have custom shop stickers on them and alot don't.

Do all custom shop pickups have identifying marks on them?

What should I look for to tell me a loaded pickguard is un molested?

Hi there. Fender only put stickers on their after market pickups so if you buy a custom shop don't expect to see any stickers on them if they do chances are they are not original.
Most standard custom shop pickups have cloth wiring.
Also specific models will have certain characteristics e.g 50s and early sixties have black bottoms while the later ones have grey. 69 s generally ( but not always ) have AYs initials on them.
Some do have additional identifiers like the Texas specials which have a blue or red dot to identify their position.
If it is all original the soldering on the switch and pots will look pristine and unmolested.
Hope this helps