Sounds like you've got it pretty well figured out. What about a small (3 step or so?) folding ladder/step stool that you can stow next to it, or under the lower bed. Then snap it out when using the upper bunk. That way you can easily move it from side to side as needed for makeup duties of the bedding too.
I don't know how much full sit up is needed on that upper bed. My son (now 19 and at college for 3/4 the year) and I built a loft bed for his bedroom at home about 4 years ago. He doesn't have enough room to sit up in his. He wanted it that way so he has plenty of room underneath for his gaming area. He likes it that way and has said he doesn't need to sit up. He likes to read in bed and just props up on a couple of pillows for that.
'03 Freightliner FL112, 295" wheel base, with '03 United Specialties 26' living quarters, single screw, Cat C12 430 h/p 1650 torque, Eaton 10speed , 3.42 rear axle ratio