Now that I had the idea fleshed out, I started rebuilding it to actual scale. Here's my progress so far:
Scale Overview:
Closer look at habitat scaling:

The habitat modules are based on the modules from the International Space Station- specifically the Zvezda unit right now.
My little scale guy:
Initial Ion Thruster design:

Based on
this image I found online, these will eventually be mounted in a giant gymbal for maneauvering.
Physically there's going to be a lot of empty space on this ship to reduce mass, but I had no idea the habitat modules would be so tiny the way I had it set up so far. I'm not sure how big the electromagnet has to be to create a useful electromagnetic sail, but I thought it'd be big. Still, I may have to rethink this, or at least cut down the number of radiators...