I was going to do the same thing; Had bought another set of heads and was going to have them done, but rode a friend's Street Glide and that was that, sold the softy. Never thought that I'd do that, but I did.
Super E ran great for me...

 

Super E here. Runs like a scalded dog; no "dip".

Had a friend with a Mukini that he just couldn't get set up right. Was a nightmare.

 

Use to run S&S on past bikes. Put a Mukuni 42 on my Road King and I am more than pieased with the performance. Very crisp and responsive. Much more than the S&S IMHO.

 

Ran a mikuni on an FXR for 8yrs along with an EV27 cam, pipes, heads and pistons. It was very fast and the mikuni started, idled and ran up and down the rev range very,very well.(Smoother than the S&S). Overall, it was a very smooth and well performing carb once it was jetted. The only trouble it ever gave me after I jetted it was that there was a small screw that held part of the internal throttle linkage that came loose and had me on the side of the road till I found it. Basically I could twist the throttle and "it no worky". Took the top cover off on the side of the road, cleaned it, put a drop of blue locktite on the screw and was then good to go till I sold the bike.

Run an S&S E on stock 80" with the stock bagger grind cam for 89. Overall, it is not as smooth as the mikuni was. But it still works very well. Idle and up and down the rev range along with mpg is strong, just not as strong as the Mikuni. In the 6 years I've had it on the road, I've had to once replace the needle for the float bowl due to wear (and overflow) and once pull the carb on the side of the road to drain the bowl and clean the needle and seat due to dirt/crap in the fuel.

As was said, the mikuni has more circuits and offers better performance, the S&S is simple to work on and jet. I've been on the side of the road with each carb, I'd rather be on the side of the road with the S&S as it's easier to troubleshoot and repair than the mikuni, that's it's only benefit to me. (Plus, I'll also admit that I do like the "look" of the S&S air cleaner on the EVO way more than the standard round air cleaner cover.)

 

Same here. My E does a great job for me.

 

They make an adapter for S&S aircleaner on Mikuni.