I own a small fabrication shop selling various automotive and motorcycle parts of my own design. A large part of my business is a series of window regulator repair kits for a couple of different Jeep models, so although I am not familiar with the Viper window regulator specifically, I have a lot of experience with window regulator problems and so I might be able to be of some assistance. Based on the original post and Chuck's reply, it sounds like the Viper regulator may be very similar to the Jeep's, where the metal guide rail is attached to the motor housing via a plastic tube, and inside the regulator is a "spiral cable" which meshes with the gear inside the motor housing. (edit: OK, I just found some photos of Viper regulators on eBay and the design is indeed very similar to the Jeep regulators, so the above does apply.)
The problem the OP mentioned is exactly the same as a very common problem for the Jeep regulators. What happens is the spiral cable is worn down by the harder metal gear in the motor housing, and eventually this will cause the gear to slip on the cable, making a grinding or a clicking sound. Almost always this happens at the full up and/or full down positions. For the Jeep, the solution is to remove the window regulator from the door and disassemble it so that you can remove the spiral cable, then re-install the spiral cable backwards. (i.e. attach the opposite end of the cable to the window bracket) This causes a fresh section of the cable to be against the gear at those critical full up and full down positions, and the regulator is back to normal, at least until those spots wear away. In order to disassemble the regulator, it will be necessary to drill out a small rivet or two, but its not a difficult procedure.
In some rare cases, I have seen some window regulators where the gear itself is worn down, but almost always the damage is limited to the cable.
The breaking of the tube as Chuck mentioned is also a problem on the Jeep regulators, however if the Viper regulator is anything like the Jeep version, when that main tube breaks, usually the window will not operate properly in one direction. For the Jeeps, the window will go up just fine with a broken main tube because the regulator is under compression in that direction, however if you try to lower it, the cable will just feed outside of the regulator through the break unless you press down on the window glass at the same time. Based on the original post though, it sounds like the window still works fine, but is clicking at the full up and full down positions. Based on my experience with the Jeep, this would indicate a worn spiral cable as opposed to a broken main tube.
I hope that helps!
PS: I just did some searching on the 'net and Viper window regulator prices are absolutely insane! If anyone is faced with a $1,000 repair bill for a broken window regulator, feel free to contact me. Sounds like the Viper may need a window regulator repair kit also.
I'd be happy to work with some beta testers to develop one. However, many window regulator problems (the clicking noise in this post or a broken tube) can be fixed for free (or close to it), so depending on the exact nature of your problem, a specific "repair kit" might not even be necessary, but I'd be happy to help, even if its just to dispense advice.