Wow, interesting setup 
. I haven’t uploaded using either arduino or windows. There are some other threads on this forum where I give some details on how to upload to apm. I use make from the command line. The code was an experiment, and I really suggest upgrading to the newest version of ArduSub: http://ardusub.com/.
I will update the readme on my ardupilot-rov fork to indicate that it is deprecated, was experimental, and I will not be providing further updates. If you are determined to make it work, try the discussion here: Problem with running BlueROV - #5 by jwalser
And let me know if you still have issues.
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-Jacob