No one's going to be malnourished. I don't know how it is in Newport, but in Pensacola all the food was pretty high in calories (deep-fried Southern cuisine), and they're going to give you ample chances to hydrate (and yes, they'll give you appropriate chances to make a head call).
If you're running 2-3 times a week and you're still borderline on the PRT, you need to be running more times per week, especially if you're prior enlisted. Speaking as a non-prior, the priors had a tougher time in OCS, because the assumption was that they should know better. OCS isn't the fleet.
As far as "distinctive" sneakers, there's nothing to say you can't wear them. Most likely, no one will care. That said, if you suck at PT, it's a thing the DIs might pick up on.
Finally, show up in shape and always give it 100%. You might not be the fastest or the strongest, but if you show up in standards and work hard, you'll be fine.