I'm thinking about the possibility of setting my IT400F (in the future) with lighting that is run off of a rechargeable battery that isn't tied into the bikes electrical system. Set up the battery in the back where the IT tool bag goes, run headlight, tail light, brake light, and maybe blinkers off it it. Would need to rewire everything independently. Have a switch pod on the handlebars for blinkers and hi/low beam.

Anyone done anything like this?

Yes.  Used Hi Cap RC Nicad packs.  Low wattage LED's.  Works great.