Here's what I think happened (based on the photos)
Warning: I believe this was Manslaughter
1) Jodi was photographing Travis in the Shower, dropped the camera or did something that made him really angry (or perhaps he did something that made her really angry).
So, she causes about $6000 worth of damage to his car, and he lets it slide, but she drops his camera a couple of feet onto a soft bathmat, and he attacks her? That isn't very consistent.
2) Jodi reacted and grabbed the knife that was in the bathroom (used to cut the tie-ups).
What tie-ups? I may have missed the tie-ups being entered into evidence. I remember her claiming that he declined to let her tie him-up, so she volunteered to be tied-up. Although, I don't recall the rope or whatever material they "used" to tie Jodi up being found in the apartment.
3) She began to stab him, they struggled (the defensive wounds come in here), the knife slipped.
Her testimony was that she had to leave the bathroom to get the knife, which she claims happened after she had already left the bathroom to get the gun.
4) She ran for the bedroom with a very angry-looking (but likely in-shock) Travis chasing after her (the massive amount of blood in the hallway happens here).
Most of the blood in the hallway is either on the right hand wall, all the purple smears, drips, runs, and splatter, or it is along the left baseboard where she drug him back to the shower. Most people in shock gradually become more lethargic or wonder around in a daze. The right hand wall looks like he used it to keep himself upright as he tried to make his way toward the bedroom. It does not give the appearance of a man chasing someone down the hall. You can see by the two purple smears down near the outlet just before the carpet that this is as far as Travis made it. One trip down the hall, and one drag back to the shower.
5) She grabbed the gun and pointed it at him (and I believe it was in place, not brought by Jodi - there are too many .25 calibre guns in Arizona to force the "stolen" theory).
You believe this despite there being no record of him ever purchasing a gun or any of his friends that he went to the range with knowing he owned a gun. If someone buys a new gun, they want to shoot it at the first opportunity. A .25 does not strike me as the type of gun Travis would buy. He owned a BMW, had a rather nice new camera, his closet was lined with nice, maybe not super expensive clothing, but good quality clothing, and other nice, good quality items. Then he went out an bought a .25 caliber pistol? They are not really good for defense, they are not powerful, they are not reliable. A .25 does not fit in with his persona. It would be an inexpensive gun to go shoot, but according to his friends he never did. Jodi just happens to be the only person in the world that knows that he owns it and just exactly where he keeps it. That'a a believable story.
6) He ran back to the bathroom to escape - and to retrieve the knife (again trailing large amounts of blood).
If he was trying to escape, why did he not go down the stairs? He would have been able to hear her jumping up on the shelf to retrieve the gun, which was close to the closet entrance to the bathroom. So, why, if he was closer to a viable escape route and she was at just about the furthest point from that escape route, did he run back into the bathroom to put himself closer to her? Why did he not chase her into the closet if he was so close to her during the chase. If he wasn't that close to her, why did he not pick up the knife initially when he started his pursuit and cut through the closet when he saw her cut that direction as she went into the bedroom?
7) She chased him with the gun (leaving a hand print on the blood in the wall).
If he came back to the bathroom, to get the knife (as you suggest in the previous point), why did she not shoot him then. If he ran, she did not need to chase him. She needed to call 911 and get help since he was trying to kill her.
8) They faced off in the bathroom - with a rapid sequence of events - her wresting the knife, continuing to stab him while he reached for the gun.
If he came back to get the knife, how does she have it? She now has both weapons, experienced massive blood loss, he is stabbed multiple times, decides to attack her again after the first attempt at attacking her resulted in multiple stab wounds, and all this has occurred in what, about 30 seconds? He decided that stopping th knife is less important than getting the knife? She feels she is fighting for her life, is having to stab him how many times now in this scenario, and still has not shot him?
9) After multiple stab wounds his strength depleted. He was unable to either reach or maintain a grip on the gun (he was wet and bloody after all).
I would say that he is getting weak by this point. She really should not have to cut his throat. Since all of the chasing back and forth and the wrestling around in the bathroom has significantly elevated his heart rate, with all the stabb wound he has received, he would be pumping blood out by the cup fulls. In all seriousness, he would propably already be unconscious.
10) She slit his throat, but he continued to move, so she grabbed the gun and shot him.
So, where are they at this point? Where did she slit his throat? Are you referring to purposeful movements or involuntary movements?
Time seems to be the biggest issue for this option. Too much running back and forth, up and down the hallway with multiple stab wounds.