I have both. I have had both on dyno's on stock bike (uncorked) and 680cc bike. Bike with open exhaust of all different kinds. The Mikuni (once tuned right) is much smoother. You can tune it to perfection. That is it's down side. So many options that the average guy gives put before he gets the carburetor right. Most Mikuni's come setup for a Harley and because of this the air jet is to small and the neelde jet is way to big. Once you get the needle jet, needle and air jet right, the Mikuni TM40 is not any harder to tune then the stock Kehin. The TMR40 is a better carburetor.
If tuning is not your bag then the Edelbrock is the better carburetor. It does have a jet that is changable on there newest carburetor. You just don't ever need to cange it if the carburetor is going to stay on this bike. The needle is adjusted or changed to make all fuel to air mixture adjustments. That is the Edelbrocks down side. You can not adjust the bottom end or change one part of the fuel mixture without effecting the other.
Mikuni upside:
Way more tunable for those looking to get the most out of a carburetor. Everything is changable....everything!
Because of the tunability it can be super smooth from bottom to top.
Has a killer accelerator pump.
Does not fload the air box laying on one side and not near as bad as stock on the other. Bike does run for a little while on it's side. Much longer then stock.
More peak Horsepowr then stock or Edelbrock (if tuned right)
Bike will start first kick (Hot or Cold)
Edelbrock's upside:
You can tune the fuel mixture anywhere any time, only need tools to lift the gas tank to get to the knob.
Bike is major forgiving for altitude change. Has about 5,000+ foot change without loosing to much performance.
Easy to bore over to a bigger size.
Bike will not fload at all laying on it's side. Bike will run laying on it's side.
Bike will start first kick (Hot or Cold)
Easiest carburetor to use/tune on the market.
Mikuni Downside:
Need to know how to tune a carburetor.
Need tools to to take the carburetor apart to change jets.
Has about a 3,000 foot range in altitude and then you will feel the difference in power.
Edelbrock Downside:
Can't adjust all of the carburetor for special modified bike very well.
It's a 36mm X 42mm Venturi not 40mm like the Mikuni.
I am running a Edelbrock Carburetor on my 680cc bike right now. It is bored out to be 42mm. It works well but, has a lull in the 2,800rpm to 3,200rpm range that the Mikuni does not have.
http://xr650r.borynack.com/