A few members over the years have logged about their training in a chair. This guy was a wheelchair bodybuilder and this guy was a wheelchair powerlifter. Between the two of them, you should be able to cobble together some useful info.
First, get specific with the goals. If you're helping her, you can't "imagine" what she means. Laying out a specific goal is fundamental before figuring out a plan. Second, if "thinner"/fat loss is the goal, remember that nutrition will be just as important as the training.
Lastly, make sure you read this article for tips on how to handle giving her advice and how to approach this in general. Any experienced lifter, or trainer, will tell you that giving training/nutrition advice to your significant other is tricky at best, and it's stirring up a hornet's nest at worst.
Does she have any pre-existing shoulder issues or is it just a general concern in the back of your head? If there's no underlying problem, simple smart training (a well-designed program and good technique) would be the best precaution.
Though I do agree with Yogi, 5/3/1 pullovers is kinda dumb. I mean, I love pullovers as much as the next guy (ahem), but they really don't lend themselves to going heavy/low rep. It's hard to believe you can't think of another back exercise, even in this unique situation, that could be done.
5/3/1 is one way, sure, or you could consider something with more frequency like:
Mon: Vertical push/pull, moderate-heavy, 4-8 rep range
Tues: Horizontal push/pull light-moderate, 8-12 rep range
Thurs: Vertical push/pull, light-moderate, 8-12 rep range
Fri: Horizontal push/pull, moderate-heavy, 4-8 rep range
So basically: Shoulders (pressing), back (pulldowns), bis or tris; chest, back (rows), bis or tris; shoulders (lateral variations), back (pulldown variations), bis or tris; chest, back (row variations), bis or tris.
Remember that intervals on a hand bike could be as easy as X time forward, Y time backwards. Doesn't just have to be alternating slow and fast.
Instead of separate cardio sessions, you could tack on 10-20 minutes of "whatever" after each lifting session. Maybe invest in some boxing mitts and gloves and let her hit the pads. Does your gym have battle ropes? Or medicine balls and room to throw them? Resistance bands for a circuit/complex?