Will these thoughts go away?

Dopamine is responsible for regulating our brain's reward circuits. When we engage in an activity that produces that dopamine release, our brain strengthens the circuitry and enforces that this is a habit we need to keep doing for our survival, even if it really isn't. So over years of repeated PMO, your brain has hard-wired the habit into your brain as a necessary habit for your survival. It's up there next to your desires to eat, sleep, and procreate.

Over time, with abstinence from PMO, the circuitry will no longer be activated, and so it'll decrease in strength over time, and that "vital for survival" habit will soon become something that you want but don't feel a need for. Then it'll downgrade to something that you remember being nice but you no longer want. Eventually, the desire will be pretty much replaced by a return to a normal sex drive that revolves around physical contact and not P/M.

It takes a long period of abstinence for an old habit that's been so strongly wired into your brain to decrease.

There's also a saying with regards to habits/addictions: "Neurons that fire together, wire together" - so other things that correspond to your PMO habit, like your internet browser, the place/computer on which you watched P, the times of day in which you watched P etc will all create urges/desires initially, because they've been wired into those same reward circuits that tell you to PMO. Over time as you spend more time around those stimuli without any presence of PMO, they'll stop being a part of those circuits, and you'll stop associating your browser with P etc.

 

Depends on your situation.

If both you and her are comfortable with avoiding it - or at least avoiding orgasm, it might be wise to start off that way - as some of the benefits of a reboot come from the avoiding orgasm part, not just the no P/M, and it'll help you reboot faster - however orgasm from sex and orgasm from self-stimulation are very different animals and really I wouldn't call it grounds for a reset, although if you plan to reboot while still having regular sex - the usual 60-120 days might not be long enough.