What do I do if I have an unaligned machine?
Send it to the manufacture!
Unless you are a very experienced mechanist and have worked on faceting machines, do not touch it. This kind of job needs to be done by somebody that knows how, and is familiar with your machine. Believe me, it is not worth the time and trouble (not to mention you might void the warrantee if it has one) by trying to fix it yourself.
Most manufactures are more than happy to do a tune up on your machine, and often all it will cost you is some shipping (and a week or so) to have it aligned. If there are parts that are worn and need replacement they will do it, and you would have had to ship it to them anyway.
If you are like me, what you really want to do is cut stones, it is much more practical and faster to have the pros do it for you, so you can get back to cutting.
Note: If you are new to faceting and have bought an older used machine and you are not sure about it, I encourage you to have it checked by the manufacturer. The machine maybe fine, but you really should have it checked before trying to facet on it.
As a new cutter you will not have the experience to know when you start to have problems (you probably will one way or another, it is part of the learning process) whether or not it is you or your machine.
Having the machine checked by the factory before you start will, not only save you a lot of trouble if it needs tuning, but tell you that the problem(s) you are having is the person at the controls, not the machine. Knowing the machine is correct will go a long way towards pointing you to where the problem is, but how to get help fixing it or learning what you are doing wrong.
It is well worth a few extra dollars to have your machine checked before you start, or if you are in doubt.