Does DAU have a formal transition plan document template that lists the key elements needed when taking a project from RDT&E phase to operational use?

Sounds like an Acquisition Strategy.  JCTDs have a Transition Manager who handled that aspect. Slides 24 and 25 of this attached hyper linked brief may help.  It also relates JCTDs to MTA. 

https://www.dau.edu/Lists/Events/Attachments/109/07-11-2018%20JCTD_RGallman.pdf

Other areas of interest may be within Middle Tier of Acquisition.  Section 3 Procedures discusses the both transition from Rapid Prototyping and Rapid Fielding here:

https://www.esd.whs.mil/Portals/54/Documents/DD/issuances/dodi/500080p.PDF?ver=2019-12-30-095246-043

Also, what courses on DAU would have this information?

The concepts discussed in the JCTD Transition Management Workshop might be beneficial.  See the workshop description and objectives here:    https://icatalog.dau.edu/onlinecatalog/courses.aspx?crs_id=1602