FYI - mechanical engineer here
Resonance mode is proportional to mass, so increasing mass is a way to eliminate low-mode resonance (although not always effective). Dampeners (such as epoxy) don't eliminate the resonance energy much (~10%) but that would really only help you trying to limit energy / vibration into your stand (although some will reflect back up into the machine so it does still help).
In my opinion, the limiting factor of your design is the joint between your extrusion and your base plate. The mode of a plate with 80/20 extrusion as you have it is quite low. Increasing the thickness of your base mounting plate will increase your stiffness substantially (increasing your mode away from the motor resonance) as would adding some 90 degree stiffeners to your columns. Make sure you have a large amount of preload on the bolts as well - if you can find it, use a bolted joint calculator online to determine the bolt and the correct force to apply to it. Properly tightening the bolts can drive up stiffness as well.
Cross-beam supports would also substantially increase your stiffness (column to column). I'd advising putting them mid-span for greatest effectiveness, although it might be something of an eye-sore.