After you choose what to do, the most important element of your workout will now be how long you do it.
You should work on duration before you work on anything else--it's more important than how fast you're going. If you're a beginner, be cautious and start with a few minutes, adding more time to each workout until you're up to 30 minutes.
The 'official' guidelines say to workout for an hour. Once you've stopped laughing over the idea of finding an hour for exercise, listen up: if you don't have that kind of time, use whatever time you DO have, even if you have to:
Note: doing too much cardio is a no-no as well. You don't need to kill yourself with hours of cardio--there is a point of diminishing returns, so keep it reasonable and don't forget to take some rest days.
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?