I'm looking to make a pretty quick EDF jet.. assuming all other things are equal, which would be faster? A single engine, or dual engine configuration, assuming the thrust/weight ratio is constant?

With two fans you have the weight penalty if you are going for speed
planes such as the Electra single edf unit is a very slick low drag airframe.
when you add twin tail fins and wider airframes then you have the drag penalty.
The F-16 is a well designed full scale single engine fighter. Planes based on that same plan form do
very well as models. If your favorite plane happens to be a twin you can still build it
and install a single fan, you save weight and still have good performance.
The yellow Aircraft small F-18 flys great with a single 120mm fan. Some designs like the
Mig 29 will not allow a single and still look scale but it can be done.

P. Richards aka SwatTeam

wouldnt the second fan's thrust more than make up for the weight penalty?

The airframe is everything in the sense that it will be the main hurdle ... ever seen a small 27" hotliner like the VIP Racer go like stink on a mere brushed Speed 400? Planes with a 2nd EDF unit will have a bigger fuse cross section, meaning more drag for speed.