A numeration system encodes abstract numeric quantities as concrete strings of written characters. The numeration systems used by modern scripts tend to be precise and unambiguous, but this was not so for the ancient and partially-deciphered proto-Elamite (PE) script, where written numerals can have up to four distinct readings depending on the system that is used to read them. We consider the task of disambiguating between these readings in order to determine the values of the numeric quantities recorded in this corpus. We algorithmically extract a list of possible readings for each PE numeral notation, and contribute two disambiguation techniques based on structural properties of the original documents and classifiers learned with the bootstrapping algorithm. We also contribute a test set for evaluating disambiguation techniques, as well as a novel approach to cautious rule selection for bootstrapped classifiers. Our analysis confirms existing intuitions about this script and reveals previously-unknown correlations between tablet content and numeral magnitude. This work is crucial to understanding and deciphering PE, as the corpus is heavily accounting-focused and contains many more numeric tokens than tokens of text.