Honestly, the answer is that it depends (you’ll hear that a lot in your career). A significant amount of the Navy primary syllabus is Basic Instruments and Radio Instruments (BIs/RIs). If you have quality training in IFR procedures, then you will just need to learn how to do it the Navy way. Doesn’t matter if it’s 180 degrees out from what you learned before, you must do it the way the Navy instructors are telling you to.
If you’re easily adaptable and open to criticism, you’ll be fine. If that’s not in your personality (be honest with yourself), or if the training you received while getting your IFR ticket was subpar, you’re going to have some bad habits to unlearn. That can be even more difficult than starting from scratch.
So like I said, it depends. Personally, I had my civilian ratings and licenses prior to coming into the Navy, and Primary was fun and not very stressful for me (Advanced and the FRS were much harder). But I went to a quality Part 141 aviation school and got a bachelors in aviation (which is worthless outside of flying). YMMV.
As for the vision piece, I also failed the eye exam at MEPS despite having a FAA first class medical and no corrective lenses at the time. Paying for PRK out of pocket was the best $5k I could have possibly spent on myself as I was investing into my own future. It delayed my entrance into the Navy by 5 months, but here we are 16 years later and I have zero regrets about spending that money.
Whatever you decide, good luck!