I wouldn't retake anything. I'd email the schools I'm interested in going to in order to see if there was a problem. You'd then have a time stamped written response you could fall back on if there was a problem in the future. For the ones that don't like it I simply just wouldn't apply there. I'd just study for the MCAT perhaps through a review course and maybe take a class or two in biology or something just to sweep out the cobwebs and show I could still cut the mustard.
Let it be said that I'm retaking chemistry now after having finished in 2001, but I figured it'd be best to brush up on them before moving forward. I'm taking them as summer classes and can say quite certainly that either what I'm going over now was either not covered, or I have literally forgotten all of it and the odds of that are slim.
So, remember I graduated in 1998 - so I wouldn't characterize your prereqs as "old". Maybe "Distinguished" 😛?
No seriously, we need more information before addressing this, like DO/MD, your ability to be flexible and applying broadly, etc. (forgive me if you have stated this elsewhere).
Also, do not forget the option of post-bacc coursework as well - either formal or informal - that is not towards a Master's program.