Would appreciate advice on unclogging hot end [Makerbot Replicator v2] My Makerbot Replicactor V2 constantly jams. Usually when I go to use it after it's been off for a few hours the filament has jammed and I have to take off the front fan to remove the filament. Today, after going through the usual rigmarole of having to take the front fan and fan guard off, remove the filament, cut it and then load it back in I found that there was another problem.

It appears something is jammed inside the hot end itself. When I loaded the filament back into the machine, it took it but nothing came out of the nozzle, instead it all pooled up around the aluminium mounting block where the filament feeds through.



Here's a couple more pictures, the last one is basically what happens to me on a regular basis: http://imgur.com/a/2jvnP

How should I go about fixing this? I've already cleaned the extruder nozzle, but unsure as how best to proceed with this. I would prefer to get this fixed fairly soon as I need to 3d print files for a uni assessment piece.
For molten filament to jam at the inlet to the thermal barrier tube like shown here, there must be something wrong with the cooling in your setup. The cold zone needs to be cool for the extruder to work right. It looks like the cold zone is not staying below the glass point of the plastic, so the filament softens and mashes into a jam. 

Here are some common causes of jamming in Replicator 2 extruders:


Printer's environment is too hot. If it's in a hot garage, move it indoors. If you have it inside an enclosure or cabinet, open it up to let it breathe. All-metal extruders with PLA are very sensitive to ambient temp. 
Not having good contact between the heatsink and the cooling bar. Normally, just bolting them together is fine, but a small amount of of thermal grease (like Arctic Silver) smeared over the contact surface can help too.
Not having the fan pointed the right way. You want the fan to blow ONTO the heatsink: this provides more turbulent flow and better cooling. This means you should not see the fan sticker when everything is assembled.
Fan dying and and spinning too slow. A new fan can be a good idea. (24v fans only!) Or you can try gently peeling off the fan sticker and adding a single drop of light oil (like 3-in-one) to the bearing, then re-attaching the sticker.
Using non-stock thermal barrier tubes that do not have the correct internal geometry. Lots of people sell bad tubes that don't have the "secret sauce" (internal diameter step). The four good vendors I'm aware of for this part are Makerbot, Carl Raffle, Micro Swiss, and Performance 3D. 
"Floating" the thermal barrier threads by tightening jam nuts on both top and bottom of the cooling bar. All-metal extruder designs require good contact pressure between the thermal barrier tube threads and the cooling bar, to ensure maximum heat transfer. The best approach is to put one jam nut below the bar to forcibly push the thermal barrier tube threads into the cooling bar, and no nut on top. (Using just one nut on top is better than two nuts, but worse than one nut below.)


It's also possible that there is some material partially blocking the nozzle, which is contributing to molten plastic backup up and jamming. 

What I would recommend right now is removing both the nozzle and thermal barrier tube from the printer, and either replacing them or fully cleaning them out. There are multiple options. You can preheat the hot end with the cooling bar in a vise or on a metal surface with no fans attached, to heat up the plastic in the thermal barrier tube and allow you to push the blockage through with a small allen key. Then do something to REALLY clean it out, like nylon cold-pulls, or cooking the parts in a blue flame such as a torch or gas stove. Then check for internal debris with something like a toothpick. 

Once you can see through the nozzle orifice and there's no junk inside anything, reassemble everything properly and try again.