Thanks for the post, that must have been hard given your beliefs.

At first, please do note that it's a long leap from believing in miracles/magic to believing in the christian god.

when atheists make their case, they assume a universe without miracles

It's not an assumption but an observation. You wouldn't call them miracles unless they were a gross deviation from your normal experience.

But there are a LOT of people out there claiming to have seen events that one would expect to never occur in a naturalistic universe.

Did you know that the lifetime prevalence of psychosis exceeds 3%? That's a lot of people out of touch with reality willing to claim all sorts of stuff. This is just one example of a naturalistic explanation yet you can see that it could cover many of those claims.

Luke Muehlhauser; apologies if I'm misremembering) in which he states that as a Christian, he witnessed healings he could not explain.

This doesn't mean that someone else couldn't :)

One could say that "miracles" are misunderstood natural events

I bet they're mostly events that never happened, people just claim they did. This doesn't require lying, although that happens too.

I'm aware of plenty of arguments for non-belief:

Interestingly only the first two of those seem like good arguments to me.