Duration of excercises for trap sprain

First of all thank you soooo much for this site! Ive had pain in my shoulder and neck for nearly a year now and my doctor didnt once mention a trap sprain. Even the physio I saw thought it was a neck problem and didnt give me the proper excercises which didnt help in the slightest. As soon as I started doing the trap stretches I noticed an immediate difference! The only problem is when I started noticing that when I started doing those isometric stretches it did start hurting again intermitently through the day but only slightly compared to before. Is that normal or should I just keep going going with the stretches on thier own for a bit longer? Are the tendons supposed to ache in the same way muscles do when you're trying to re-strengthen them?

Thanks a lot for the help mate. Guess if Im just pushing against a finger rather than my palm I wont be able to exert much force wil I. Any idea how long these kinds of shoulder injuries take to heal? Ive been off weights and Thai Boxing for 9 months which is killing me realy. Ive trained since I was very young you see so this much time off is a shock to the system.