The frequency of your workouts will depend on your fitness level and your schedule. Beginners should start with about 3 non-consecutive days of cardio and work their way up to more frequent sessions. The general guidelines are:
But, what if you can't follow the guidelines? Then do it for however many days you DO have. If you only have two days to workout (and you'd have to work really really REALLY hard to convince people you can't find another day to exercise, but whatever), then that's what you do. It's certainly better than nothing.
Keep in mind that if you can't follow the guidelines, you may have trouble reaching your goals. If you can't do the work required to reach your goals, you have two choices:
It's totally up to you. There's no super glue binding you to your goals and if you know you can't, (or won't), do what it takes, then why lie to yourself? Because, you enjoy living in denial, don't you? Admit what you'll really do and move forward instead of setting yourself up for failure with goals you know you aren't going to work for. And don't end your sentences with prepositions!
You say you have a 30 - 45min window of opportunity to take protein, etc. after working out. Does this mean 30 - 45mins after a complete workout, or does this mean 30 - 45min after working out a single muscle group?