"Small lip"? Any jolt can be very painful when the muscles go. I'd try for "no lip" into the shower and no threshold into the bathroom (or, preferably, anywhere else). I'd also double-check that the bedroom layout works such that there is enough width/depth to use the Hoyer to transfer to/from the wheelchair and bed, and that there is room for the hospital bed, including space behind it for using the power functions (extra space for the head).
I know Diane mentioned an overhead lift and maybe that works w/ your setup, but I would try to allow for the Hoyer as well, since we don't know what her preferences will be.
I wouldn't do the stair lift/multi-level thing.