3x6 for rabbit, ok?

It should be. She would very much like to have levels in it so she can jump around though.

Sounds great - should give your bun plenty of room to stretch out. Remember though that if you want to keep her confined you'll need to factor a roof into the design, which on a 3 x 6 will need a bit of support in the middle if you use grids. Another option is to cover the top with wire mesh, this can be held on with nylon ties. May sag a bit in the middle but you could support it across the top with a beam running from one side to the other.
Good luck!

Maybe overlapping the grids slightly and using zip ties to hold them together instead of connectors would make the roof less saggy?

Good luck on your cage! 3x6 sounds like a wonderful size.