I have the same problems, with the neck being the worst. My solution is to alternate riding my upright (tandem) with my recumbent (single.) On the recumbent I have zero pain problems. I can ride longer distances more comfortably at the same speed. If it weren't for enjoying the teamwork with my wife on the tandem, I'd be 100% recumbent. As it is, I consider it cross training and enjoy both bikes.