Issues with Stepcraft 840 ("Y" axis and heating)

I would like you to help us with the situation we are facing at the moment: at our company, we have an Stepcraft 840 with which we are having some difficulties when we upload a G-code in order to make drills, as some of them are not in the correct position.

It happens that, when we put the machine at "home" position before each drill, those drills are correctly done, however, when the G-Code isn't corrected in order to settle "home" position, the drills are not correctly done.

We think that the mistake comes from the motors, because there is a lag in the "Y" axis. Is this the real deal, and how could we fix it?

The next situation we are facing is with the 3D printing function; when we turn on its temperature control, adjusting it to the right temperature, and we wait until it reaches the desired temperature,
the whole head, including the extruder's motor and the extruder itself, starts heating until reaching a very, very high temperature. It is so high that you can smell the burning odor even from a far place (15 meters aprox.) So, what we have done, is turning off the temperature control, and hold on unktil it cools itself.

When we turn it on again, the temperature control does not work anymore, I mean, if, for example, we settle a temperature of 100°C, the extruder starts heating until reaching those 100°C, but it doesnt' stop there, it continues heating, with no limit at all, reaching so much higher temperatures than the desired ones. The temperature control only displays "hi".

We think it might be possible that a disconnected wire or with a false/poor contact may be the reason why it is happening.
Could it be the problem? How could we fix it?