Good take on the "personal relationship gone astray" aspect of the song. But I think that the biblical references are more than just cliches...Kevin Moore is much more clever than that.

I think that he merged two concepts into one song; that of a broken personal relationship and that of a broken spiritual relationship. Perhaps at the same time his personal relationship was ending, he was having doubts about his religious beliefs as well. It has been said that "Pull Me Under" was sort of a merged commentary on the lives of Hamlet and Jesus, so it is possible that Kevin likes to obfuscate the true meaning of his lyrics in this way.

Just some food for thought...

I agree with the interpretation, but i would also like to add to it. If i repeat what he wrote, sorry, but I think there were things that should be added to make it more comprehensive view of the song's lyrics. Here I go:

Daybreak
at the bottom of lake
it's a hundred degrees I can't breathe

Ok, he finally wakes up to the truth that he's in a spot that's a result of a combination of problems stemming from his woman. Lake, can't breathe, temperature, etc. serve only to show how deep its gotten. Daybreak, he wakes up and is dumbfounded on how he got to this point, and with her.

And I won't get out
'til I figure it out
Though I'm weak like I can't believe

He's taking responsibility for the situation, and making a distinct point of this being actualization. This is his turning/breaking point or climax in the relationship. Things will be different from here on out. Rather than extolling his righteousness, at this point at least, he chooses to say that this set of circumstances is simply wrong and must not be allowed to continue.

So you tell me 'trust me' l can trust you
Just let me show you

You get him saying that he can trust her, but its one sided. Its obviously a fickle trust, she is not following through.

But I gotta work it out in a shadow of doubt
'cause I don't know if I know you

He needs ground to stand on. The foundation is unsettled, and so is his perspective. If he is unsure whether he knows her, he doesn't know her. Once he stands for something, for himself, then he can see if she's true, but her power over him is leaving him uncertain of his own self. There's no confidence for his own ideas and its all going too fast, hitting him one after the other, the small bit of trust there was is fleeting.

Doing fine but don't waste my time
Tell me what it is you want to say

His patience is getting slim. She's in a similar situation herself, apparantly, and its dragging him down as well. If he's not what she wants, and vice-versa, he's admitting that wasting time is useless... this is no longer giving him any benefits, so he must either move on with the right information (her side, what she has to say), or move on alone (as hard as that may appear to him at the moment).

You sin, you win, just let me in - hurry
I've been out in the rain all day

He's turned a blind eye many times at her blatant disregard and disrespect towards him in her actions. It's time to put up or shut up for them both. He's declaring that his heart is in ruins. So, he pleads to her to either let him feel what's going on, or help him find another way out of the proverbial rain, or so long.

So you tell me 'trust me' I can trust you
as far as I can throw you
And I'm trying to get out of a shadow of doubt
'cause I don't know if I know you

He's restating the trust element because the trust he feels he misplaced his trust in someone who isn't who he originally thought. There's doubt on who she is now. Everything has a dialectic to it, throughout the entire song, and it's his humility. He's become more aggressive and more certain that he's right--that she's not exactly worth it (to put it kindly).

Don't tell me you wanted me
Don't tell me you thought of me
I won't, I swear I won't
(Did)
I'll try, I swear I'll try
(Lie)

She teases him with the words he wants to hear. He wants the companionship, the relationship, the potential that was promised. When it falls flat, almost as if it was a LIE. She isn't putting her words into action while he swore, at least, that he would try. This is a somewhat last ditch effort for her to back up her words.

Mother Mary quite contrary
Kiss the boys and make them wary
Things are getting just a little bit scary
It's a wonder I can still breathe

The contradiction to balance out his aggressive attitude is evident here. Religion, motherhood, and the balance that is there. Every person is someone's son or daughter, and every woman is potentially going to be someone's mother. The untouchable position of motherhood (and Mary's motherhood) is confusing his heart. It is also bringing back to his roots and what's important to him.

Never been much of a doubting Thomas
but nothing breaks like a broken promise

Her broken promise is making him doubt himself and what he stands for. Nothing breaks his heart like her broken promise, her broken word, her unfullfilled actions.

You tell me 'bout your two more coming
but once is just enough for me

The first commentary is suffice for this line above.

I had gotten used to being a soul destroyed
She comes in apparently to fill the void

With his heart in ruins, he's easy to quickly pick up and become used because the void feels so massive. Her potential, the words she spoke breathed life into a place where he had used to being empty.

All dogs need a leash and
at least I'll forget it

This may happen again. This may be one in a string, maybe it happened before. But he's moved on in the past, and he'll move on again, forgetting her and becoming a dog to another woman's leash. No lessons learned.

And she would never hurt me though
she's never said it

Interest of fairness, he's relegating her actions to unintentional impairments in the mixing of their two worlds. His pain--that she caused--is simply not meant to hurt him, but it does anyway.

But I'm not gonna ask her today
I don't wanna scare her away

He's allowing some space because of the emotions involved. Its serious, and he doesn't want it unfairly concluded due to fear. He wants the truth, no more lies.

Your town, I'm all alone
and I just can't stare at the phone

No more waiting. The situation won't change until someone changes it... he knows this, but does she?

I wanna talk about lifelong mistakes
and you can tell your stepfather I said so

I agree with his interpretation of this comment. In addition, there's a history of her lineage being not so storybook (as per her parents marriage falling short). He's also taking a stand. With a subtle yet brutal statement about her family/stepfather, he might also be connotating that she was her biological parents mistake that they must live with forever. But he doesn't have such an obligation with her, and he's reminding her that leaving and moving past her is possible, and somewhat likely.

I really like the "stepfather" part, opens up a whole new meaning to the word. I guess I thought he was, in the context of the song's meainig, an expendable character with some inside story behind his inclusion in the line (there probably is either way).

KM rules

I think the "stepfather" line could be a reference to Mike Portnoy's stepfather, who didn't have a very good relationship with MP at all, as described in the song analysis of Honor Thy Father.

I know the song was written by Kevin Moore, but just a bit of input from a new DT fan.