Should I insulate my rafters in addition to the ceiling in an unconditioned attic?
You should not. Because the attic is vented, the upper insulation does almost nothing. In the summer at the attic will get much hotter than it does now, increasing cooling costs.

Also, you would be creating what's known as a hot roof. This can be damaging to the roof sheathing and shingles.

Most truss bottom cords are 2x4. This is normal, and the insulation usually reaches much higher than the tops of the ceiling joists. The usual routine is to raise the floor with additional framing to allow for more insulation.