Welcome hypochondriac!
It sounds like getting sober is the key...... Have you considered inpatient treatment? Or used any other resources (like AA, other programs, etc.)?
Things will only get worse if you keep drinking. I got migraines as well, and towards the end of my drinking I developed a tremor in my hands and had soreness in the area of my liver. Since I stopped, everything has resolved itself.
For what it's worth, I though I was functioning "just fine" too..... I think I felt that as long as I kept up appearances, I wouldn't have to give it up. Now that I can look back on it though, I was a lot less functional than let myself believe.
Living sober is so much better..... I hope you give it a try!