Ahhh, the carb question.
I am thinking about changing carbs on my fxr4. .... I know many people that run S&S carbs, but a friend of mine that works at the local Harley shop says that mikuni carburetors are the way to go. I will eventually have the heads reworked, a better cam installed, and ignition changed, and maybe high compression pistons put in. So does one carb work any better than the other when doing these mods?
To start my $.02 worth, AMP wrote what I have been told by experienced HD techs.
S&S carb will work great(probably the best) for wide open and top HP applications. The Mikuni is more "fine tuneable" for everyday riding. It gives you a smoother fuel delivery, more controllable.
However, those same techs went on to ask me if I really needed a new carb...what kind of riding was I going to do and how far was I going with my motor makeover? Because they could re-jet my stock CV to match the heads and cam just fine.
I have SE heads (instant 9.5:1 compression) stock pistons and bore, EV27 cam, SE lifters, SE ignition module, coil and wires. I went into this project with a Mikuni carb on my wish list but the techs talked me out of it. They agreed that I could save myself $500 by re-jetting the CV carb. What AMP said is apparently true--more tuneable, better fine adjustment, more even fuel delivery. Theyre great carbs. But I had to ask when I was going to "feel" all that with my riding style. There's something really sexy about those Mikuni carbs, while S&S seem to be thought of as oldies but goodies, but I have to say my motor sure does run good with the re-jetted CV along with all the then-new performance parts. Would it run better with a Mikuni? Possibly so, but would it be $500 better? Those Techs don't think so and 1 1/2 years after the motor work I see no need for a carb upgrade.
Just thought I'd throw this into the mix. One thought would be to do the other mods you mention first and then see if you still feel the need for a new carb. Me, I'd prioritize the mods in order of impact. Cam and heads first. Unless you're going really radical with those, I doubt you really need a new carb.
Of course, this is just my opinion.

[edit]
HOwever, it's not just my opinion. I checked the nightrider.com website (lots of good info) and found the following pertaining to the stages of high performance builds for Evolution motors. They don't recommend a carb change until stage 3 and even then, well, read for yourself:
http://www.nightrider.com/biketech/hdbuildstage3_95.htm“If you don’t have the money to purchase all the parts listed for this engine, we recommend you make the following changes:
Use your re-jetted CV carburetor in place of the Mikuni HSR-42. The CV is capable of supporting a 90 HP engine. Just keep your Screamin Eagle air filter clean and make sure the carburetor is well tuned.”
If a 95 HP Evo with lots of heavy duty high performance mods (read their list for this stage and stages 1 and 2 before it) doesn't need a Mikuni, then I know mine doesn't.