All you can say though is that at 2948.5 "full repairs [are] in progress." They could have been in progress from the moment Kirk made the previous log entry and this log entry would be the same (assuming that they were still in progress).
2945.7 - Finney dies (1.6 digits to >)
2947.3 - initial log entry / starship status chart
shows NCC-1701 to be 83% complete (1.2 digits to >)
2948.5 - full repairs in progress / "couple of days" (0.4 digits to >)
2948.9 - repairs almost complete
Even if we were to assume that the ion storm took place in the same system as Starbase 11, interpreting this as a repair status chart would mean that
- it took the original repair crew only 1.6 digits to do 83% of the necessary repairs, but with the "help" of the extra crew
- it took them the same amount of time (1.6 digits) just to get the "final" repairs / 13% done!
Maybe that's why Stone is no longer in command of a starship.
And what was Spock doing all these days (?) with the computer logs? His arrival in Stone's office clearly shows he's late and was expected. This has all the elements of a ship that has just arrived, but not one that's already harbored at Starbase 11 for a couple of days.