Hi Geno,
Yes, you should be able to do much of that using ReefMaster. We have a bottom-composition module that creates E1 and E2 (roughness and hardness) layers which can be exported as Shapefile polygons for use in ArcGIS. Also the bathymetry can be exported in the same way, or as an ESRI grid for further processing in ArcGIS or other applications. At the moment RM cannot get bottom hardness data over the ethernet - we only support NMEA 0183 for live mapping (which only has position and depth data), so for bottom hardness and sidescan you would need to record your sonar data to an SD card before processing it in RM. This might preclude the use of your separate GPS when recording bottom-type and sidescan data for use in RM, unless you can get that signal into your HB unit, but the GPS on the unit is probably good enough for your needs.
Another issue might be correcting for location with your towfish - we do have transducer location offset settings, but the relative position to the boat is not going to be constant during turns - although you can mitigate this by doing straight runs.
We also have a sidescan mosaic module due for release around the middle of this year.
I would recommend downloading the trial and seeing how you go, and then coming over to
our forum where there are plenty of mapping enthusiasts - you will get a quicker response to your questions there.
cheers,
Matt