I'm gonna go through this line by line and tell you what I think, OP:

He was very upfront about it though in person and basically explained that he was being stalked by a crazy ex.

He lied and tells you what sounds plausible, that's nice but all the stuff you talk about later sounds like overkill just to avoid a crazy ex.

He doesn't have a smart-phone and is uncomfortable around mine. Whenever we have convos that are personal he asks me to turn it off and take the battery out.

What kind of personal stuff? There are only a few groups of people he could be hiding from when he tells you of this: government or organized criminals.

He said he was self-employed and worked on computers. I didn't want to be nosy and pry.

You live with him so you get to be a bit nosy now. Just don't sound hostile when you talk about it.

He freaked out when I used one of his computers in a pinch once.

Could've been configured to be a honeypot like someone else in the comments said.

The day after I totaled my used car, we went to the dealership and he bought me a new car, in cash. He didn't even talk about it with me. He just kept saying he wanted me to be safe and that used cars were dangerous.

In another comment you've mentioned that his mom is living in a house he owns. A lot of this stuff sounds overkill even for those of us who care a great deal about our own privacy. Yes, you should consider your own privacy compromised. You're gonna have to ask him some questions but don't ask in a hostile way. Ask him what he does, and how all his security stuff works exactly.

Maybe he is crazy paranoid, but that does not necessarily mean he's dangerous. Maybe he isn't paranoid and he is hiding from someone, or a couple of someones. If he's doing all this because he feels he's in danger, then that means you might also be in danger.

As for the money and how he gets it, maybe he buys and sells exploits (questionable), or maybe he's a cyber-criminal of some sort. Or maybe he's a foreign spy.