1. do you have a split system
or package unit
on the rooftop (im thinking you referred to a rooftop (packaged) unit. what size unit do you currently have (thinking 5 tonish)
2. Any chance of building in a soffit in the bathroom or using flex to move the return line.
3. is the 'in the way duct' the main trunk (from the orginal 2)you spoke of or the third.
There may be another place to tap a return in the home as well. It could also make the unit work better and that would definately require some experienced eyes to look over and do some calculations..
Last idea and its a wild one. If you are going to replace the unit at some time in the future and going with a split system. Air handler in the closet and condenser outdoors. Reason I say this is I have returns in my concrete floors and LOVE them. I have 3200 sq ft and run two 3 ton units with 30 ft ceilings. The concrete acts like a precooler for the air and I get a 10 degree drop at the return just from the air going underground.