First, the technical stuff. Don't be too overwhelmed -- I'm bored and a literature geek, a bad combo. And as always, feel free to ignore anything I suggest, my ego is far too hefty to be impacted

Scowling then closing her eyes she inhaled a deep breath
Sounds a bit awkward, I'd insert a couple commas at least, or revise the fragment. S/A "She scowled, closed her eyes, then inhaled a deep breath"
un unattainable
bible
-> Bible
A strange and slightly jarring transition from P2 to P3; the first mentions "sweet revenge," but the next starts out calling it an ugly emotion, graphically.
No-one may not enter the kingdom of heaven
Very awkward double negative.
Her fresh and lovely face now contorted,
The "Now" seems to imply a transition back to the present, ie after the murder; I'd suggest removing it.
gapping
-> gaping
his now aged body
The "now" again sounds awkward, implying another shift in time that isn't supposed to be there.
phallic
-> phallus
stockng
glasping, and unglasping
Glasping?
unfinishe
snear
hesititated
his minded raced
-> mind
Nake
she now slide those
-> slid
hime
Instincitively
And, his ankles
Technically a sentence should never start with "and;" you can break that without much problem, but the comma should go -- it initiates an unnecessary pause.
large sideboard cupboard.
Too many boards.
There shall there be any more pain
Awkward
Rebecca, leaned over him,
Remove the first comma
euphorisa
thoughts of task
insert "the"
glisteing
Tomorrow he would be a repentant man, now however, powerless to defend himself against her wicked temptation he took a deep breath and, like so many times before, he prepared to allow himslelf to be taken by the pleasures of the flesh.
Change punctuation to: "Tomorrow, he would be a repentant man; now, however, powerless to defend himself against her wicked temptation, he took a deep breath and like so many times before, prepared to allow himslelf to be taken by the pleasures of the flesh."
Rebeccas
fot he
<The cross, the symbol of suffering, her suffering each time> he coerced her into that that musky smelling room to be alone with him.
Sentence fragment; needs a verb. "was"?
She stood up, and walk
no comma, walk -> walked
crusaifix
than 'crossed' herself
-> then; no quotes around crossed, it's not a euphemism
Turning, back towards him,
Remove first comma.
whispered a pray
-> prayer
contored
sobbed, like
no comma


End of the technical part


To answer your questions, while it's not particularly hard to follow I don't think you should jump around so much. Specifically you give away the beginning and end in the first 1/4 of the work, which means the rest is just...the rest. It leaves an incomplete story arc and leaves a very unsatisfying ending (we know what the future brings; we just read it; we don't even have to think about it for a second once we're done reading). The intro is very good, and I like the idea of beginning with the end, but when you start your flashbacks I'd highly recommend making them sequential. Particularly, although you alluded to it you never used any of the "little girl" flashbacks to actually add to the plot; either remove them all or utilize them to tell the story instead of the memories of the "earlier that evening" time frame.

I can visualize some of what's going on rather graphically; you got the gore down well but other than 'he's between her knees' and a brief mention of her poise near the end, you never actually say what they look like. At one point his blood spattered in her pubic hair and I was surprised to learn she was nude (it was mentioned in a later time frame, but not that one).

For all that, I was very impressed with the work. You're a great author, and this has a ton of potential. I think you stretched a bit too far to create an intricate structure at the cost of the story (as your question implies you already know), and that needs either some more tweaking and transitioning or a reworking to prevent interference with your story. That you came up with the structure at all and made it work reasonably well is a testament to your imagination and skill. When you pause to focus on description your language is amazing; a couple more pauses is all that's needed for elaboration. Well, and a quick spell check

I'd definitely read this just for pleasure, and I look forward to seeing what you do with it!