Pilates Tot......my first response in reading this is.....and if I would have been in person with you I would have said, "stop---if you feel pain, stop". Stretching past comfort level can be uncomfortable, but pain----in my book----isn't great to work through. Regarding the neck and shoulder tension......this could maybe be avoided by bending the elbows a little bit (if you weren't). Again, without seeing your form in person, I can really speak to what you may have been experiencing. One suggestion if you were to try this active hamstring stretch series again would be to use a yoga strap/belt maybe to allow for a bit of leverage with your arm support and holding of your leg. You may be able to approximate your shoulder position easier for less tension in your neck and shoulders.