"a fraction of the time" isn't a very clear problem statement, as 9999999/1000000 is a fraction, but that's certainly not what is meant by the common sense understanding of this phrase.
I am wondering what we can do without clarifying the statement further.
We can still encode 90*60 23-bit vectors and have the friend pick the one, in the remaining time after he finishes, that minimizes the distance to the true answer, but without knowing how early he finishes. That is probably still the way you can get the best score on average, but I don't think it does better for the guaranteed number of correct answers than just transmitting 1 bit of information (which guarantees at least 12 correct answers).
Would it help to use odd vs even seconds to indicate whether the fiend finished early enough to use the clock to indicate an arbitrary time vs the time at which he should have left was already gone when he finished his exam? I can't think of how to use this (or a similar) signaling to improve the worse case odds.
On the other hand, while I cannot think of a way to improve your worse case situation, you should be able to improve average score by sorting your 5400 23-bit vectors so that the distances between the last ones are as large as possible.