Do I treat this as a continuation of the previous relationship or an entirely new one.
I'd view it as a reboot. Like a new relationship that is informed by past experiences. It's been a few years so some things might have changed, some things might be the same.
How do I separate the negativity from the end of the relationship from the stuff created by my mind in the 3 years after that.
How much of this is my own demons to battle and what should be shared with her?
This is why I suggest working with a poly counselor. You can share that you are in therapy and will bring things up as needed. And the therapist can guide you on what should be just you and what should be shared with her.
The counselor might also help you decide if you even want to do this reboot in the first place. Or if it's too many things, too many years, too much stress, etc.
Do I bring up the past in an attempt to avoid the same pitfalls
If you decide to date again? Yes. Bring it up. See what growth there has been on both sides.
Could talk about the LDR issues and how it might play out today.
It's not "negative" to want to know what you are getting into. It's not "negative" to want to prevent problems and have clear expectations of each other.
Like if she had a problem with being punctual in the past and you would get tired of waiting around for her to show up on dates? You might learn that since the break up she's got an ADHD dx. To deal with her "time blindness" she now uses alarms and other tools to help her be punctual. (One of my kids has this.)
She doesn't know exactly in either case. She said her feelings just sort of faded, but couldn't explain why. And then they slowly came back. Again she's not sure of the reason. I have a few hypotheses, but I don't really want to interrogate her on them.
Was it NRE fading? The limits of LDR dating? Something else?
My ADHD kid waits 4 months before asking someone they are into out. It helps them make sure they are actually into the person and it wasn't like ADHD hyper focus or something. When they hyper focus on something it runs hot for about 3 months and then drops as fast as it came on. Hence their personal decision to wait 4 months to be sure the interest is still sticking around.
I'm just not very experienced in getting back together with someone.
It's ok not to have much experience. Ultimately, you are still the one who gets to decide where you want to invest your time and energy or not.
GG