Sorry if this is a bit off the core thread of using Reefmaster for the Sidescan mosaic for Archaeological mapping topic (Matt if you feel this is too far off topic feel free to pull it down)
I too have been using Side scan sonar to find and document shipwreck sites for a number of years (I use an old Klein 595 Side scan) but in addition to mosaic software I have started using
Structure from Motion to document the specific sites. I feel this may also be of interest to some of the responders to this topic.
Basically it provides a automated way to get photo mosaics of the wreck/area of interest similar to the images below comprised of around 500 odd individual images
or
I have mainly collected the raw images as a swimming diver but have also collected the base images from a diver scooter and a small ROV
Sorry for the redirect but have a look at a thread at
OpenROV on how I have been doing this if you are interested in the technique
Scott