My guesses, and that's all they are without more history/exam.
Atopic dermatitis.
Morbid obesity. (you said so yourself.)
Poor posture, or you sit incorrectly for long periods, causing nerve impingement. (pins/needles/numbness/headaches)
No exercise. (see item 2) General malaise.
As far as the exam, you may be asked to disrobe but with your undies on. If they want to check your pubic/anal region they will have you remove them at that point. Don't worry, they have seen it before, trust me. If you are worried about your penis size just go in with a woody and say how excited you are to be there.
Most of the exam will be basic stuff: weighing, blood pressure, temperature, general background questions. <--that is usually done by the nurse or medical assistant. The doctor will review that info, ask you some more specific questions and then do an exam. They will probably: listen to your lungs, palpate (feel) your neck, chest, back, abdomen, as well as some percussion. (they lay one hand and tap on it with the other, gives density info of internals.) Also, they will look in your ears, eyes, nose, throat. Since you are over 40 the doc will probably do a prostate exam, don't worry, you just lay on your side on the table and it's over before you know it. (except for the slimy butt, yup, I said it.) Probably send you to a lab, if they don't do it, to have a general workup of your blood done.
After that the doc will speak with you again and go over any concerns and/or findings.
Kudos for finally going, if nothing else it will stop your worrying.