I would like to put the lat long data right into the JPEG images though.
  I don't know how to use gpsbabel or any other program to integrate the
  lat lon in the EXIF part of the photos. I can use the commandline if it
  is required or if there are a few simple commands. 
  Maybe a command could be:
  exiv2 -a 01:02:03 ad *.jpg

Install exiftool; it more or less will do what you want, with a time
offset and writing exif geo tags from a gpx.

From the man page:

            The "Geosync" tag may be used to specify a time correction which
            is applied to each "Geotime" value for synchronization with GPS
            time.  For example, the following command compensates for image
            times which are 1 minute and 20 seconds behind GPS:

                exiftool -geosync=+1:20 -geotag a.log DIR



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