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There is an annotated photocopy of the Grove article "Sources, MS. II.5. Western plainchant, 12th century" in the Keeper's desk (bottom drawer) with pencilled-in annotations of Isham call numbers for those items Isham owns in reproduction.
A large gift of microfilms was presented to Isham by Professor John Milton Ward IV. There is a blog post about these here: http://blogs.harvard.edu/loebmusic/2011/01/05/john-ward%e2%80%99s-treasure-trove-of-microfilms/ The post includes a PDF inventory.
Manuscripts
Here are some ideas for how to discover music manuscripts at Harvard:
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