Fitness can be pretty complicated but it doesn't need to be. Here is the Joe Collins Fitness Model in a paleohack post. If you are doing more than 4 things at the gym at once, you are wasting your time. You need a lower body movement, an upper body push, an upper body pull, and a conditioning drill.
Lower body: Deadlifts and Squats. You are having issues with your hands right now so you can work on the leg press machines. Some gyms have the ones where you lay on a sled and push yourself or the weights and then there are the machines that have shoulder pads where you push up while standing. Either works. The wrist straps would work out very well if you want to do deadlifts. You can get the gloves with the straps on them. I don't like them long term but if you are having issues with your bones presently, it can help distribute the weight more evenly so each bone feels less stress.
Upper Body Push: Bench Press and Overhead Press. These exercises usually have machines at the gym and while I abhor using machines with all my soul, it would be a good first step for you because of your bone issues to just get into a strength training routine. Eating a proper diet and getting some strength training in might help your bone density and allow you to get off the machine and onto free weights.
Upper Body Pull: Pull-ups and Rows. If you can't do pull-ups or are having grip issues, the lat pull-down cable machine works well and you can use the wrist straps as well. Same as rows, especially if you are doing dumbbell rows.
Conditioning could be some rowing or swimming, some tabata intervals or Crossfit MetCons or something short and intense of the sort. If you have issues in the past with chronic cardio, keep to these guys and keep them brief. It will do your heart better anyway.
I would avoid the treadmill to warm up. If you have stress fractures in potentially all your toes, running sounds like a horrible idea. Rowing might be tough on your hands but the wrist straps can come into play at first and you don't need to grip that hard. Swimming is a great work-out because it works both conditioning and strength and it has some pretty practical skillsets as well. Unless you work on the 29th story with a broken elevator, the Stairmaster doesn't have much of a real work skillset to it. Use some mobility drills, Scott Sonnon has some great work on it, to get your joints healthy and muscles warmed up. Do that instead of running to get going.
Right now, my "splits" are deadlift/overhead press/ pull-up/lat pulldowns one day and bench press/front squat/rows on the next day. I wish you all the luck and please ask more questions if you have them. Haven broken my foot before, I know how frustrating things can get so I really hope that your change in lifestyle will lead to a longer and much happier life.