If you could accelerate two beams of protons in the same direction near the speed of light would the magnetic force created by the particles overcome the elecric repulsion, allowing the particles to collide?

Yes, see:

 

http://lhc.web.cern.ch/lhc/

 

THE LARGE HADRON COLLIDER

I don't see how the LHC link addresses the question - is there a physics link I didn't see that explains it? (The LHC will use counter-propagating beams, so I wouldn't be surprised if there isn't.)

 

Parallel currents attract. In accelerator/beam physics, I believe this is called the "pinch effect" at least for a single beam (i.e. view one beam as two halves and they should attract and "pinch")

my thought process on this is that you have two particle accelerators, and im not sure how these work exactly and stuff, but two that accelerate to near the speed of light of a current or stream of protons. Lets say that at the end of the accelerator the two streams are parallel and a meter apart and then leave the accelerator. would the magnetic forces caused by the two particles force them to collide and ultimately fuse together?

Probably not fuse - I don't think you'll get a force large enough to let the nuclear force manifest itself.