<p>My MakerBot 2 jams after a couple hours of prints. It is a couple months old, and the tip stops extruding after a couple straight hours of prints. I am guessing that there is a design flaw and that the media is melting inside the extruder before the feeding teeth. Does anyone have experience with this?</p>

You may wish to consider
Craftware
for your purposes. It's a free program in beta form that does provide a tool-path animation for printing the layers. It is not so much specific to a printer as it is configurable for your own requirements.
The video
shows what I believe you are seeking at about the two minute point.
Simplify3D also provides such information, but is not a free program.