<p>I have been running my i3 MK3 for about 12 hours now and the motor on the extruder is fairly hot, not too hot to touch but I'd guess its about 60c on the outside. Is this within normal operating temperatures or should I let it cool down before starting more prints?</p>

The maximum operating temperature can be found in the specifications of your steppers. Usually the ambient temperature operating conditions are limited to 50 °C with a maximum operating temperature in the range of 70 - 100 °C. For instance, the steppers I use are limited to a temperature of 80 °C. It is however advised to keep this temperature lower, e.g. to max. 60 °C to prolong the life. Do note that very high temperatures could be a problem for "self-printed" stepper mounts of the wrong material (materials with a low glass transition temperature).
To answer your question: "Yes, steppers may get hot, but if you want them to get too hot is up to the mounting system and how long you want to use them."