I assume that the sensor is 'square' with the camera body and lens. The front of the macro lens can thus be treated as parallel to the sensor. I mount the camera on a Manfrotto levelling base attached to the camera standard or holder of a copy stand. I can then lower the copy-stand standard until the front of the lens sits on the negative carrier. (I use a 35mm carrier from a 4x5 enlarger for this so that the lens is on metal all the way around.) With a little fiddling I can get the front of the lens perfectly flat on the lens board when the levelling base and standard are locked down. Then I raise standard to the height I need. (The upright for my copy stand seems to be sufficiently square with the base not be add more complications.)
For a light I use an LED head made for 4x5 enlargers. Conveniently, its top is parallel to the diffusion plate on the bottom, so it sits securely upside down on the copy stand.
Zig-Align is one of those things I would probably be tempted to buy if I saw one 'in the flesh', but I've never been sufficiently annoyed with alignment to order one.