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You can easily modify the Milestone column to contain the word "Milestone" plus the indicating letter. Transpose the other columns, with the Problems columns as the Data fields and the Program and Milestones as Key fields.
Another Formula tool adds the Milestone text to the Name column (so you'll have Milestone A Problems Resolved).
Finally, a crosstab tool lets you summarize by Program, with the columns you want.
Dynamic input can remove the underscores, if you want, and a Select tool will rearrange the columns.