The removed D is likely a grease strike, but remotely possible could have just been removed with a knife and some skill.
Your photos are great, but still a shade too blurry for the other thing. Your coin is a 1941-S large mint mark, and the DDO-001 is on this. Kinda looks promising as it's a very light doubled die but might be showing on your coin. Something to look into with your coin in-hand.