When transcribing I found it very useful to keep a couple of transcription aids open on my web-browser. The two I found most useful are below:
The Index of Scripts on ‘Medieval Writing’
The index itself is vast to the point of daunting if you can’t already identify the script you’re working with. However, with perseverance you should be able to find a page that will help with your deciphering. The website offers a letter-by-letter index of many different scripts up to the 16th Century.
http://medievalwriting.50megs.com/writing.htm
Harvard’s ‘How to Read Medieval Handwriting’
This is a much briefer (and therefore more navigable) introduction and a good place for beginners. It explains some of the essentials of medieval handwriting and a list of common abbreviations which is particularly useful. It’s also worth scrolling to the bottom and investigating the pages on ‘Scripts’ and ‘Textual Instability’ which give engaging short introductions.
http://isites.harvard.edu/fs/docs/icb.topic453618.files/Central/editions/paleo.html#top