ok, so according to my sister at an unnamed Auburn insurance agency; If the modifications are permanantly affixed to the vehicle, they should be covered in the event of a loss. Something like an XM radio which is removable, is not covered, as it is not "part of the vehicle".
And she also mentioned that if you feel like you aren't getting anywhere with the insurance adjuster and/or company rep, call the Maine Bureau of Insurance and let them know what is going on, and why you, as a consumer, are not being treated fairly.