A few months ago I bought an FXR3 and it had a mild cam, ported heads, Crane ignition and V&H Straightshots. It also had an S&S E carb with Thunderjet.
I took the E off and went with a CV. On a dyno I doubt there is a HP difference. The E has sharper throttle response, but not so much to be worth the purchase price if I had to buy it. At least not to me. The Thunderjet killed the mileage. It got 40 MPG, and went to above 50 with the CV, an issue with the small FXR gas tank.
So for me, if the bike came with a Mikuni I'd keep it. Or if I could find one cheap, maybe. I like the CV. They are cheap, they work well, and compensate well for altitude if you ride the mountains. The big problem with the Mikuni is that there are too many tuning choices (I never thought that could be bad) and sometimes a good change here might cover up a bad one there and you might have a tough time getting it fine tuned.
YOu can find good Mikunis on eBay for not a lot if you are patient.
I have a nasty Mustang with an aftermarket Double Pumper carb. The carb has removable idle and main air bleeds and four corner idle screws. I put in smaller air bleeds and had to open the jets and turn the idle screws out. Larger bleeds, the reverse. I screwed with that thing for over a month and finally gave up. Too many choices and me with no AF meter and nary a dyno within 100 miles.
My best thoughts on this:
Keep it simple if you bought it to ride and not to tinker with.
Since you already have the CV I'd tune it correctly (not hard) or if there is a bike event nearby or a good shop, spend $60-$100 or so and have it dyno tuned. Then never give it a second thought. You'd likely get more power out of the $100 dyno tune than the $300-500 Mikuni anyhow.
Bullwinkle