Sam,
The reason the doctor is telling you to listen to your body is because TBI's and PCS is near impossible to fully understand --the reason being, no two cases are the same. The symptoms I have, you may not - the treatment that helps me, may not you.

Telling you to listen to your body, is their way of trying to have you self-regulate... which can worsen your symptoms because the increased anxiety/ocd/stress of trying to figure out what works/what doesn't/what is making matters worse/what helps... increases brain stimulation, thus worsening your symptoms/intensity of symptoms.

I had mild ADHD before my TBI and after it became pretty severe. I originally could deal with it with exercise, later around 27y.o when I wasn't as active as I was in college, but still exercising regularly - they put me on a small dosage of Concerta. After my injury they changed me to Adderall. Post injury, I suffered from insomnia. Initially, I wondered if the adderall was contributing to that. Be cautious of the time of day you take it, also is it an XR or IR form you are taking. What are the milligrams? What does your daily diet look like?

As for the working out, and delayed onset of headache. It isn't in fact odd to have it delayed. For some, the onset of a headache or increased intensity of a headache with exercises is immediate, usually do to hormone secretions and/or blood pressure changes. However, it is common to have delayed onset of headache. The reason for this is the way your body is balancing hormones to return to "homeostasis" as well as some other possible contributions. I would ask, are you male or female? The hormone levels in males vs females varies, and changes with ovulation. The levels also change with exercise differently with males/females. Are you working out in the morning, afternoon or evening? What is your activity level post-workout? Are you going home and resting, are you starting homework, are you going to the mall, watching tv, etc. -- meaning, what is the brain stimulation post work-out? Also, are you listening to music/watching tv/talking while working out, or is it just you and aerobic exercise? Is it only aerobics you are doing, or are you adding in resistance training - such as, is the bike at general speed or are you adding resistance to it? Are you walking on flat ground or are you adding hills?