At times, it was somewhat difficult to "endure" braces after my splint therapy. What I found particularly difficult was having to wear an expansion appliance to expand my upper palate (which was too narrow). Every time I had to expand the appliance with a little "key", I felt like my head was splitting in two for a couple of days. I persevered though. Fortunately, that part of the orthodontics only lasted about a month.
I did find at times that braces did cause minor flare-ups of some symptoms - headaches, light-headedness, sinus pressure mainly. These flare-ups usually occured for a period of a few days after the routine adjustments to the braces. I found the intensity of the flare-ups increased some during the time I had to wear the elastics. But none of the flare-ups compared to the pain of my TMJ prior to beginning treatment. My dentist also stated that I seemed to be one of those patients who are very sensitive to the forces exerted by braces.
Hope this helps,