I was in a similar situation many years ago, working for a small firm where I had excellent rapport with the boss. I went from salary to getting paid by the hour as well. I didn't want to work 60+ hours a week. As it happened they got a client close to where I lived and I was able to service them very well, by being a "local". And after a year, I was making 50% more, before expenses, and working less hours and minimal commute time. It was a win-win-win. Happy me, happy client and happy boss.
Every situation is different, but my experience shows that it is possible to re-negotiate stuff as long as you are good at your work and can demonstrate a win-win.