Its already broke in. Had my first oil change about 6 months ago. The high RPM thing is when it shifts. The RPM is higher than before it shifts. Where before it felt right when it shifted. It also feels like i have to push the gas pedal down a lot more before it starts moving. I would go as far to say it feels like t's slipping than catches than moves or shift to the next gear. Never did this before. It started last week when my wife ran it through a mud hole.
Did your wife have it in High Range and get stuck and really hammer it trying to get out? Particularly in Reverse? Do you have heavy/larger than 27" diameter tires?
If so, you likely have a burnt clutch. A symptom of that is a RPM spike just before shifting as the glazed clutch plates don't have the same coefficient of friction that they previously did and they spin until the clamping force of the transmission is great enough that it causes them to "bite" and engage.
Before I got carried away though, I would check some of the things mentioned above and make sure that your oil isn't contaminated, make sure you don't have any loose grounds (under the driver seat rubber flap), and maybe even do the clutch initialization procedure. However, assuming you are still under warranty, I personally would probably take it to the dealer and let them look at it first and see if anything could be covered under warranty.
If it is a burnt clutch, Honda needs that data point to make sure they get a fix in place. People will take these things in the mud and people expect the same level of reliability as the Rancher and the Rubicon, that is why they buy Honda.