My questions are: Is it okay if I'm not hitting my target goals, like fat is a few g under if protein is too?

Listen to what your body is telling you, watch your weight on the scale, do what is best for your body per day. You should be able to feel what your body is craving.

If you workout and your muscles hurt you need protein. If you aren't feeling full you need fat. If you're feeling exhausted you need calories and the right amount of carbs to boost you back up.

I'm using carb manager to track everything should I be logging my vitamin supplements I take with my prescription meds?

Vitamins are good, I'd ignore.

Can I start working out whenever? (I can only elliptical and treadmill at this time until after some upcoming surgeries)

Thanks for your tips and tricks