Currently I am running RS-38 carbs. Before that I had a set of RS-36 carbs from the eighty's . My bike ran great with the old RS-36 carbs but they developed a hanging idle problem that I haven't been able to solve yet,so I bought a new set of 38's a year ago. The 36's ran perfect with the factory recommended jetting and needle settings. The thirty eights have required different needle settings and main jets to run right. I don't know if I'm getting more horsepower with the thirty eights yet I'm still playing with the main jets. When I put my flatslides on my yellow fj1100 it went from being much slower than my black fj1100 with the flatslides to being comparable to it. I highly recommend them.
I ran 36, 38 and 40's. In the end I stuck with the 38's for years. The one change was a different needle jet. The RS's are the "small block Chevy" of carbs. I currently run FCR's which are great but are more complicated to tune.