Headache & Neck Pain

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Nothing wrong with stretching, but the first money I'd spend would be on a good bike fit. Ask around for a fitter in your area who's experienced with women riders and with the type of riding you like to do (some fitters think only in racing terms, which might not be what you're after). Glad you've found a way to stop the headaches for the time being.

I agree that you should ensure your bike or another bike properly fits you. Good bike fit should enable you to ride for several hrs. without neck /shoulder pain or having headaches. It doesn't sound quite right that you have a need to stop and stretch during a hill ride.

Keep up stretching before and after cycling.

Are you relaxed on your bike wherever you ride? Meaning your handlebar grip not tight? Your handlebars should be shoulder-width..

My bike (Trek 7.2 wsd - straight handlebars) was fitted at the LBS, though when I would go uphill (before this all happened) I would throw my butt back off the seat and lean down and yes, I would hold the handlebars in a death grip while looking at the top, thinking omg, when will it ever end!! This, definitely un-relaxed position I would get myself in, I am assuming, had a lot to do with my neck pain, sigh. Now, when I go up hill, I look just beyond my handlebars, I don't (well try not to and if I do, I correct it) scrunch down and slide back and hold onto the bars for dear life, instead I stretch my back out long and loosen my grip, bending my arms a bit and it is making hills somewhat easier, I think...
Hopefully I won't have to always stop halfway to work my neck and shoulders, but I think am kind of doing it as a preemptive good luck charm superstition thing, those headaches were so bad, I'll do anything to not have them come back!