Well, it kind of sounds like you are already on your way to figuring out what you want to do. Are you planning on doing an upper body day on Friday as well or just go one day a week there?
I guess my main question would be, exactly what lower body stuff can you do at home? Do you have dumbells to do lunges, step-ups, etc. with, or are you doing everything with the Bowflex? I'm not really familiar with what you can do with that, but I'd imagine you can figure out a way to use the cables for leg variations.
Maybe something like this:
A. Single-Leg Superset
Simply pick any single-leg exercise. To make it posterior-dominant, widen your stance, to make it quad-dominant, bring your feet in closer, don't lunge at as far or step up as far on the box, etc.
B. Cable Pull-Throughs
I'm assuming you can do these with a Bowflex, if not, I'm not sure, you'd have to think of something else that hits the glutes/low back that you can do with the machine.
C. High-Rep Calf Work
If you have dumbells you can weight it, but if not just do high rep bodyweight calf raises or single-leg calf raises.
D. High-Rep, Unweighted Ab Circuit
A. Bench Press
B. Lat Pulldown
C. Tricep Extension
D. Bicep Curl
I'm assuming you can do all of those on the Bowflex?
B. RDL/Good Morning/Back Extension
C. GHR/Leg Curl
D. Weighted Abs
A. Bench/Incline/Military Press
B. Bentover Row/CG Supinated Lat Pulldown/Chins
C. Front/Lateral Raises
D. Reverse Flys/Face Pulls/Shrugs
If you aren't planning on lifting Friday, I guess just throw some of the shoulder/upper back stuff in on Tuesday.
I don't know what your goals and whatnot are, so I just kinda came up with that off the top of my head, but I hope it helps a little.