Basically what I'm asking is does roblox's physics engine handle motor6d's differently than it handles welds? As in is there any difference in rendering or performance? I'm asking this because I'm animating a gun and I want to know whether it would be a better idea to use Motor6Ds over welds because the script updates the C0 and C1 properties of the weld every 1/60th of a second.
I just need to know the primary differences and similarities and the effects both have on performance and rendering, thanks.

4 comments
Can't answer for sure, but I've often heard from other developers that Motor6D's are fastest joints. I haven't researched my self, so I can't answer why it's so.
Yes there is a difference.. One major difference is the animation Editor can work on Motor6Ds, which means less coding, and possibly a reduction of margin of error for it. http://wiki.roblox.com/index.php?title=Animations#Playing_Animation_in_Non-Player_Character
Benchmark it ;)
To be clear, since Motor6Ds and Welds share the same set of properties and methods (sans the Angles stuff for Motor6Ds), it shouldn't be too hard to switch between the two on the fly.