The datum of the plane is not arbitrary and it is set at a particular line of the fuselage. The designer of the plane would have already determined where that is.

There is no real point setting the firewall square and then measuring from that as you don't know how many degrees down thrust has been built in.

I wouldn't assume just because the bottom is flat, it is parallel with the datum. Most models tend to taper up at the back.

You need to find out from the manufacturer (if you can), where the datum is. If the plane has a flat canopy base, then set that to zero and measure everything from there. the stab should be zero. Failing this, I would do the following, but you can use it to double check as well.
Set the plane up on a balance stand and set the stab to zero degrees. It is more than likely that it has been set at zero. Move the balance stand so that the plane sits at this level with no support under the tail or nose. Mark this point on the wings and you can work out the percentage of the MAC. You can now measure the wing incidence and down thrust. Also check that both stabs and wings are set at the same incidence.
If you have a true flat surface, then measuring with a steel ruler and using trig. can be very accurate. I did it that way for years. just be sure that the ruler is exactly vertical when measuring.

Hope this helps.