I think you need to step back and take a deep breath. You have a lot of different problems to solve and you need to take them one at a time. You have a lot to learn so you are going to have to take a systematic approach.
Limit switches. The machine will run without limit switches. Just set the machine 0,0,0 at the corner of the table, and then set your part on the table at that corner. Or set the part on the table anywhere, and set 0,0,0 to a corner of the part. It is only important the the CAM 0 and the part 0 agree. Make sure that your CAM Z zero and the machine Z zero agree, normally would be the top of the part.
I would start out with a simple 100mm square, and just engrave the profile. Set the Z 0 above the part so you can air cut rather than actually cut. This will give you a chance to get the machine under control before you actually try cutting anything.
It sounds like you can't even get the machine running. Does the software that came with the machine actually run G-code? And do you have a method of getting G-code into the machine controller? If you can get the machine running at all, then that is a good start. You can do an upgrade later. Normally a G-code file has a tap, nc, or cnc extension. The controller proabaly won't like a stl file.
The easy way to do a tool change is to do all of the machining operations as separate programs. That way Z goes to a safe position and you can jog the machine to a good position to do a tool change. If you don't move the part then the machine still knows where everything is, but you will have to zero the Z again. There are better ways to do this, but let's start simple.
To separate text and engraving from machining operations, you should be able to put them on different layers, or at the very least generate the code as separate operations by selecting only the items that you want to machine in a given operation.
This should get you pointed in the right direction.