For me (personally) is counting calories really easy. I am from Germany and there is a smartphone app called "FDDB Scanner". It is really simple with this app. I am pretty sure a similar app exists in other countries. I know there exists also a Facebook app called "Cronometer" to count calories. In my opinion it is really helpful (maybe you try it least for a few weeks to get a "feeling" on what/how much you have to eat).
I prefer to work out between the 2. and 3. Meal. Generally i work out 5-7 times a week. 5 times when i am doing "normal split training" and 7 times when im doing "highfrequency training" (i dont know if you have heard about it).
I dont care too much about the time when i getting protein. Everything in between 2 hours after working out is ok for me. Maybe its better to get it directly after working out, but i am not a professional bodybuilder, so i dont care about it