[extent]

I did not tram the head (the 3040 construction makes this almost impossible anyway...)

Tramming the gantry is half difficult, tramming the head is dead easy.

Getting the Z axis squared up along Y you just need to shim the base of the gantry. Just need to take a little care that you don't twist it, check with the head on both sides of the gantry to make sure that it's shimmed evenly.
Getting the Z axis squared up along X is harder, you have to take a lot of the Z axis apart to get to the bolts that hold the Z axis on, and they're on quite tight. That one I left alone
Tramming the spindle in Y is trivial, shim the spindle mount
Tramming the spindle in X is trickier, but not excessively difficult. Loosen all of the spindle mount bolts slightly and tap it to twist the mount. Carefully retighten the solid side of the mount to hold it in position once you have it.

With all of the bolts, you may have to drill the holes out slightly if the part you're moving is binding up and not moving far enough, especially the spindle mount. I had to file them quite a bit to allow the mount to twist enough to align straight. Also try flipping your spindle mount upside down if you're really far off, that got my machine a lot closer to trammed before doing any major adjustments. It only takes like an hour or two to do, and I was able to remove something like 60% of the factory misalignment.