Two invaluable online resources that have been lifesavers for me as I’ve started to work with unedited manuscripts:
A. Cappelli’s Dizionario de Abbreviature – The indispensable and definitive guide to Latin abbreviations, this online version of the Italian edition is much more comprehensive than the later English edition.
Enigma – In what I can only imagine was the result of an inspired friendship between a medievalist and a computer programmer, this brilliant tool allows you to enter as much of the word as you can make out, together with a host of wildcard options, and then provides you with a list of every possible option, courtesy of Whitaker’s Words. Particularly cleverly, it allows each minim (the identical vertical strokes found in ‘i’, ‘u’, ‘m’, and ‘n’) to be entered as a ‘!’, so for example, ‘!!!!!!!ere’ spits out only three possible options (innuere, munere, numere) which you can then narrow down based on context.