A missile system like the SA-6 is not composed of a single, autonomous vehicle. A full system requires target acquisition radars, target tracking radars, a launching vehicle and a crew of qualified operators to make everything work. Unlike an IR SAM, succussfully employing a radar guided SAM is an incredibly complex operation. The systems involved are fully integrated and not easily converted for employment in ways other than their original design. In other words, you can't just take parts from a system and create a "mini-launcher." The Navalized versions of SAMs are similar to their land based counterparts, but since they don't have to be air transportable, or autonomously mobile, they tend to be even larger and more complex.
With all that said, if a SAM had been responsible for the downing of TWA 800, the evidence would have been obvious and undeniable. Even the smallest SAM warheads are designed to direct thousands of fragments into the targeted aircraft with the hope of puncturing some vital system. And the missiles either hit their target, or they don't. Picture a target hit by a shotgun at close range. When the target is the size of a 747, if the missile functioned at all, the aircraft would have been peppered. Not punctured by one or two rogue fragments whose impacts left no evidence.
>>A missile system like the SA-6 is not composed of a single, autonomous vehicle.<<
Right, two autonomous vehicles, connected by a single cable or data link. If a battery can "relocate to an alternate firing position in approximately 15 minutes", set-up can't be too complex. Iran's military has employed the SA-6 for quite some time, so skilled operators or training would not be a problem.
http://www.fas.org/man/dod-101/sys/missile/row/sa-6.htm
>>...if a SAM had been responsible for the downing of TWA 800, the evidence would have been obvious and undeniable. Even the smallest SAM warheads are designed to direct thousands of fragments into the targeted aircraft with the hope of puncturing some vital system.<<
True. If all the sheet metal in the aircraft's vital areas, such as the fuel tank, had been recovered and was available for independent inspection, I might be looking at alternate explanations as well.