I used to have the same problem. What helped me was to lower the seatpost a cm or so, raise my (quill)stem a cm or so, and bring my saddle forward little bit(2.5mm maybe). It made a pretty big difference.

I don't think track or trackish bikes were really meant to be comfortable over long distances, but they're fun as hell to ride. If your hands are lower than your butt, you're going to experience discomfort eventually. Even just to look up to see traffic. Risers can bring your hands up, but leave you with only one position. Everything's a tradeoff, ya know?

I can say that my angus has felt very comfortable since I got it to the point where my saddle is close to the same height as my hands. What is it Mike Watt said? Something like that.