MEPS is a day long process, 5am-2pm'ish. PFA should take a half hour...its a 1.5 mile run, 2 minutes of pushups and 2 minutes of situps. Scheduling this stuff is what takes long, so that depends on you and your recruiter. For example, I was ready to take the PFA the day I set foot in recruiter's office, and that was like 2 months ago. I'm still only tentatively scheduled to actually do it this week.
As far as eye surgery and other ailments...you tell them at MEPS, they're probably going to want to subject you to more eye tests before they give you the all clear...I have 20/20 so I don't know details of what that may be, but expect to go through MEPS and have them say they want XYZ more tests done and medical history stuff before they clear you...who knows how long those can take. Then again, if you pass the vision test with no problems, they may not give a crap if you had it or not...there's really no way to tell, depends on their mood that day I guess. I'm not a MEPS doctor, so I don't know for fact.
As for the school and GPA thing, I graduated with a 2.993 GPA. However minimally below a 3.0 I was, it was still below a 3.0, which everyone says is the benchmark you need to at least hit to be competitive...on the flipside, it was from a top tier business program, so that probably accounts for the slack. But there's no formula to determine it.
I had 2 military reccomendations: one was my dad's cousin, the other was a friend's uncle (we had met briefly)...both were O-6's, Army and Navy respectively. I had a couple profs write letters, as well as the dean of my school, which ultimately served as mainly extras to bolster my app. My two really important ones were my employer references, which I am convinced sold it to the board...the reason is that they went beyond the standard letter of recc prose "He's extremely athletic and intelligent, has high moral standards, uses good judgment in stressful situations, etc" and went into detail about ways I had really shined when it came down to the wire, my abilities and how I was able to compose myself when faced with adversity, what that meant in terms of leadership. Those are really the things only someone who has known you for awhile could attest to, or at least someone who has been through the trenches with you, regardless of their background. In my case, an engineering employer and an advertising planner aren't exactly military, but I think their recc's carried the most weight in the long run.
As for your profs, they can definitely tout the rigors of the academic program and thereby attest to the intelligence it takes to be successful in it...it couldn't hurt to reach out to them and sit down to discuss what you're tryign to do. Most will find it incredibly admirable and will be willing to write you something intense and characterizing, regardless of how well they may have actually known you (as was the case with my profs and the dean of my school). But moreso, best to get someone who can fill that letter with substance, regardless of their background.
For extra-curriculars, they like sports. Competitive sports means you value your physical performance and health, and can call upon it in times of need. I personally think people generally respond well to physical prowess, which is why it is a good telling of leadership potential...my personal views on why I think physical is important.
Can't offer any advice on the taking PFA abroad or MEPS abroad, I just don't know how that works.
Other than that, you're probably not going to change your grades by that much, and you can't make up for not doing a ton of extra-curriculars over the last 4 years in one year. All you can do is go into battle with the weapons you have, and hope heart and determination combined with your other strengths pull you through. You'll never know what the board is looking for that day, what they would say no to, what would sell it to them...just gotta make that packet as strong as you can and apply, and probably say a prayer or two just for good measure.
Good luck