shoulder and neck soreness after swimming

I've just started training for my first triathlon this year, and have been doing some light workouts in the pool for about a month now. I was on the swim team in high school, but I haven't done any lap swimming since (about 10 years), so I'm definitely taking things slow and working on making sure my form is good before I up the intensity. My main issue has been that, despite feeling fine/great when getting out of the pool, as I get further into my work day, I notice my back between my shoulders and my neck feeling sore or stiff, and this eventually leads to a headache (I'm one of those people where sore neck = headache). Since this has started, I've tried paying special attention to my alignment and breathing, applying hot or cold to my shoulders after my swim, and making sure to stretch my neck and shoulders during and after my workout. Nothing seems to get rid of this problem altogether, although it might be getting a little better since my headache doesn't come until towards the end of the day now rather than before lunch. My next thought was to try strengthening those muscles on my non-swimming days, but if that doesn't work I'm really not sure what else to try and I can't keep this up if two days a week my workday is a bust because of a headache. Oh, and apparently pain killers don't work when it comes to neck-related headaches for me.

Has anyone had a similar problem, and how did you fix it? Or any other thoughts?