OK, I have made a stab at creating a custom PRJ file to get it to work.
Here is what I created:
COMPD_CS["NAD83(HARN) / Florida East (ftUS) + NAVD88 height",
PROJCS["NAD83(HARN) / Florida East (ftUS)",
GEOGCS["NAD83(HARN)",
DATUM["NAD83(HARN)",
SPHEROID["GRS 1980",6378137,298.257222101,AUTHORITY["EPSG","7019"]],
TOWGS84[0,0,0,0,0,0,0],AUTHORITY["EPSG","6152"]],
PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],
UNIT["degree",0.01745329251994328,AUTHORITY["EPSG","9102"]],
AUTHORITY["EPSG","4152"]],
PROJECTION["Transverse_Mercator",AUTHORITY["EPSG","9807"]],
PARAMETER["latitude_of_origin",24.33333333333333],
PARAMETER["central_meridian",-81],
PARAMETER["scale_factor",0.999941177],
PARAMETER["false_easting",656166.667],
PARAMETER["false_northing",0],
UNIT["US survey foot",0.3048006096012192,AUTHORITY["EPSG","9003"]],
AUTHORITY["EPSG","2881"]],
VERT_CS["navd88-12b geoid height",
VERT_DATUM["North American Vertical Datum 1988",2005,AUTHORITY["EPSG","5103"]],
UNIT["metre",1,AUTHORITY["EPSG","9001"]],AUTHORITY["EPSG","5703"]],
]
However, the program keeps giving me an error message stating "Unsupported Vertical Datum". Even the stock NAD(HARN) + NAVD88 Height that comes with AgiSoft Photoscan gives me the same message. I have all of the NAVD88 geoids downloaded into the geoids folder. I'm not sure what I am missing here. Any help is appreciated. Thanks,