Potential popcorn thread...
Here is what I did. This is assuming your carbs are squeaky clean.
Fitted larger main jets (in my case 130, I would think 125 would be fine to start with).
Move needles up by one notch from stock. PD41s have adjustable needle clip positions which makes life a lot easier. If you have PD42s you will have to shim them. Do a search, plenty of 'how to's' on the site.
I stayed with stock pilots, but have them turned out 2 full turns (as opposed to 1 3/4 stock).
How does it run? Pretty good, anything above 4K rpm and it absolutely flies. Lower down pretty acceptable too but will never be as smooth as a standard set-up. I suggest you have a good read of all the pod threads on here, there are loads of variables and you need to be prepared to invest the time in getting it right. There's a lot of folk on here who don't think it's worth the hassle, and I can understand why.
Before you do anything you need to find out why your bike is running rough. 3K tune up is a must, verify your ignition system is operating correctly, timing is good and you have a good spark on all cylinders. Make sure you haven't got any air leaks on the intake rubbers. With your carbs, check your accelerator pump is working properly and that the fast idle cam is set. Did you pull the pilots? You can't clean them properly without doing so and if clogged they will affect the idle. Synching is the very last thing you do, it shouldn't matter what size main jets you have in there as they will not be coming into play at idle speed.
Best of luck and welcome