You freed up the springs so they move as needed, the shock you have can may not be able to control the bounce. I would pull one off and see how much effort it takes to move it through it's range of motion. When you moved the fuel tank and battery, you shifted a lot of weight to the rear, this will also effect how the shocks work.
Hows the driveline angle, did you change it?
Mine runs smooth with the same basic set up, fuel tank behind the axle, tube shocks, and teflon spring liners. I also removed three leafs for a soft ride.
Joe
