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So I've got an issue - the hot end is spontaneously cooling. It might get through a few layers and then it will start dragging the plastic. And it's only the hot end that cools down. In repetier, both the bed and the hot end are still turned on, but the temperature for just the hot end drops. Earlier had an issue with the F2 fuse shorting out, but now it seems to be working. I checked for shorts and found a loos connection with the heat0 on the motherboard, but thinking there might be an issue with shorts in the hot end, though I haven't found anything at this point. Anyone else having a similar issue or might be able to give me some advice on diagnosis?

Sounds like you've got a bad connection somewhere. If it only drops after printing a few layers there is a good chance it is at one end or the other of the heater wires in the umbilical. A loose crimp will cause this. If you also see it occur with no movement (just set the hot end temp and let it sit - does it drop after a few minutes?) then I would double check the RAMBo connections. If the connection is failing as the wire heats up, damage is occurring. Look for shiny insulation or stiff wire. Both are indicators that the insulation has overheated.

Are the layer fans running? If so they may be cooling the hotend.
Solution would be wrapping the heat block of the hotend with several layers of kapton tape or the self fusing silicone tape.