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"What is the Talmud" by Eliezer Berkovits states:

The only complete Talmud manuscript is in Munich; besides that only larger or smaller fragments have survived. In his “Dikduke Sofrim,” (Munich, 1878-1897) Rabbi R.N. Rabinowicz lists only 39 fragmentary collections of manuscripts.

This links says:

All known manuscripts – some sixty-eight in total...

So how many manuscripts are there of the Talmud? And are there any recourses (books etc.) that deal with the number of manuscripts that exist and that detail the differences in the manuscripts (other than Dikduke Sofrim)?

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The Friedberg Jewish Manuscript Society's Hachi Garsinan project seems to offer what you are looking for.

To quote from their blurb (emphases mine):

The Hachi Garsinan site displays all variant-readings of the Talmud Bavli, including images and transcriptions, with sophisticated comparison tools between the variants. The "Hachi Garsinan" site is meant to serve the wide range of all Bavli learners and researchers: from academic researchers, through Yeshiva communities and Torah students, as well as anyone interested in exploring the variations of the Talmud Bavli and its transformations throughout the ages.

The site contains high quality digital images of all original textual witnesses that exist for the Talmud Bavli (manuscripts, early printings, Genizah fragments, binding fragments and other fragments), accompanied by precise transcriptions of the text in the image. The site integrates additional functions, including full text search, Sussmann catalog, Dikdukei Sofrim, and also save, copy and print options.

From the website, here is a list of currently known "complete" manuscripts, by tractate. (As mentioned by Harel13 in a comment, many of these manuscripts have come to light only in the 100+ years since R. Rabinowicz compiled Dikduke Soferim.)

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