Pictures would be helpful.
Sunken chest and protruding clavicles: more calories and more compound lifts. Concentrate on bench press, pull-ups, dips, military press. If you are skinny, your bones will be obvious.
No, right now I've just finished writing a novel, so I've been doing a lot of sitting, not much time in the gym. I've got a home set up with a bench and some barbells and a couple of kettlebells just to keep me going.
You need to do lower body. Not only do you need to keep balanced, but the lower body workouts are the ones which produce the highest amounts of testosterone, which will help everything. Squats give you bigger biceps.
A good basic routine with compound lifts like squats, bench, deads etc should only take about half an hour in the pit. Go heavy and then go home.
Unfortunately, the shape of your abs is mostly genetic. If you don't like them, your best bet is to work on some other body part which looks better, so it will distract the eye. No-one else will be as critical of your various bits as you are.