1) Just because she may have arrived in Mesa around 4am doesn't mean TA knew it, she had a different car with possibly no plates and likely parked down the street to avoid detection and then just helped herself into the garage to wait until the roommate left. It's more than possible she fell asleep while waiting and then let herself into the office to poke around, find the camera, inspect the safe, etc until she heard TA in the shower.
2) I feel pretty confident that as forgiving as TA was, even he was past that. In fact, the angry texts may even have been about him finding the nude pics.
3) See above, he was trying to move on without her, he'd made that pretty clear.
4) TA could only delete the ones he knew about, I wouldn't doubt she'd collected what she could if only for blackmail, see 2.
5) The problem with this is that all of the nudes were in unallocated spaces and therefore the dates all came from Encase(see my above post) and the times of those would also be consistent with LE's work hours. The shower pics were only deleted so their exif data was intact and Encase was able to pull the actual dates and times from that.
I know either scenario is possible, but sneaking up on him unawares in the shower introduces an element of unpredictability as to his reaction and risks putting him in an alert and defensive state of mind. Even though he was vulnerable in the shower either way, if he had by chance spotted her from ten feet away, out of the blue, he would immediately be on the defensive and aware that she meant him harm. Much better to get him accustomed to her presence with a false agenda, trusting and vulnerable, and turn on him at the best possible moment, when he was the most helpless and unsuspecting. She knew how to manipulate him, and I believe she would use those skills rather than just sneak up on him like any random intruder.
Your point about the roommates being home at 4am and having to wait until they left is a good one, but it was a weekday so they were probably gone by 8 or 9am.