I have never heard of someone being charged with having burglary tools for having a crowbar in their car. I actually have one in mine. No good reason for it TBH I just bought it for a project, took it where I needed for my project and never took it out once I was done. I honestly can't think of a single legit reason for it to be in my car. I spent 6 years around a 911 center and not once in my life did I ever see a car accident where a life could've been saved if someone had showed up with a crowbar so that's a highly, highly improbably scenario. Still it harms nothing so I carry it around 'cuz I'm too lazy to move it someplace else.
The cop telling you you can't have a flashlight is an idiot. If you had a baseball bat sitting on your passenger seat would that be illegal? Of course not. And a baseball is designed specifically to club things. That is it's purpose in life. Having a club is not illegal. Clubbing people with said club is. I'd like to see what law says you can't have a club in your car 'cuz I can club someone with anything I've got in my car. I wear suits. I have neck ties in my car. I could garrotte someone with one of them. There are no laws against such things and the officer who told you so was an idiot.
I'm still looking for an argument on how registration of guns is discriminatory at all. The presumption of innocence only applies to those who have been legally accused of crimes. No one has done that here.