Yes you can, and this is a common step that many folks take when building a rig, especially with non-stock suspension and shock mounting points. I did this with my EB's frame when it was in about the same state of assembly as yours. Its really pretty easy.
First put the frame up on jack stands, with the stands supporting the frame itself, letting the axles hang down freely. For the front, you can just remove the coil springs and cycle away. The springs don't provide any "control", or spatial locating, of the axle assembly. The rear is a little trickier since the leaf springs are also the "control" links of the rear suspension. That is, they control the location of the axle assembly as it cycles. So you can't just remove the whole spring pack. But you can unbolt the spring pack and only use the main leaf. Get some blocks (wood would suffice for this) to approximate the thickness of the removed leaves and bolt it back together using only the main leaf. Now you can easily cycle the suspension by hand. You will of course get more droop this way, and the spatial location through the suspensions travel won't be exact compared to with a full spring pack, but it will be close, and good enough for this purpose.
Good luck, you're going about it correctly (actually cycling and measuring rather than guesstimating)
Dusty