The difference in version between V1 and V2 was due to 2 things. First, the hotend was changed from the older Buddaschnozzle style hotend to a hexagon all metal hotend. The Buddaschnozzle by default had a 0.5mm nozzle, the Hexagon ships with a 0.6mm nozzle to compensate for the smaller melt chamber area. They also removed the fillament tensioner post from the V2, as it was apperently not really useful. It is difficult to use the buddaschnozzle with a machine that contains hexagon firmware, as the thermistors are incompatable, so you have to change firmware to go back and forth. the V2 keeps the machine using hexagon hotends.
The clip insert cannot damage your print head. Even if you got it wedged into the hobbed bolt, the hobbed bolt would just eat it. If you still want to try it but are worried, there are alternative extruder bodies that contain a section nearly identical to that wedge built in. http://www.thingiverse.com/thing:1355145 for example.
The flexistruder has a teflon tube liner that allows for smoother flexible fillament feed. You can print and make your own. You will need some specialty drill bits and teflon tube from Mcmaster carr, and a small drill press is required, but you can source all of that for under $100 assuming you buy a harbor freight mini drill press for $50, under $50 if you already have a drill press. Here are the complete step by step instructions. https://ohai.lulzbot.com/project/lulzbot-taz-flexystruder-v2-assembly/
There also is another flexystruder. It is experemental. It is also fairly expensive to put together. It does feed with more force through the nozzle though. http://www.thingiverse.com/thing:1201229