The larger displacement, cam, etc. ought to leave the cylinders sucking on the carb harder, which would deepen the vacuum and make all the existing jets pass more fuel along with gulping more air.
Although the pilot jets are pressed in, they are what is called a swagged fit, or interference fit. They can and most certainly should be removed for cleaning and inspection. Grab them with soft jawed pliers and yank them straight out. I've done this to each and every PD carb that has crossed my bench for attention. After cleaning as any screw type jet would be, they simply tap right back into the same swagged hole until they seat on the shoulder feature machined into the jet brass.
However, there is no reason, at this time, to replace them with another size, as it has yet to be proven whether the pilot screw adjustment range is currently insufficient. That will be determined near the end of carb tailoring/rejetting, with that throttle response test I outlined.
With the changes you made to the engine's volumetric efficiency, there isn't a single factory book value spec that can be relied upon to be correct for your set up. You have effectively re-engineered a portion of the machine, and since the carbs aren't smart enough to automatically adapt to the changes, you will have to find the correct adjustment and metering values for each of the three fuel supply devices inside the carburetor. You may even have to change the float level and or emulsion tube holes or the slide needle taper, to make all throttle positions achieve ideal fuel ratios.
I don't expect you will get it perfect, perhaps close. But, I'm pretty certain that unless you like lottery odds, you will not get it correct without placing the machine into controlled test conditions, getting some feed back from either a dyno fuel map printout, or loading the engine on a test track and reading the spark plug deposits for combustion deposit residue, to determine a direction to change the fuel metering closer to ideal.
Perhaps I've misunderstood the problem. Are you saying you've been happily riding it about, happy as a clam with all operation parameters and something suddenly changed?
Has it had issues for a while now and they've gradually deteriorated to become unacceptable?
Have you checked the spark plug deposits to see if it has slowly built up enough carbon to begin misfiring and develop poor idle traits?
How have you determined which spark plug heat range is proper for the new configuration?
I guess I may not be able to help you further, as I cannot ascertain bounded data with which to formulate a corrective approach.
I do wish you luck in random changes and casual driving about for testing. But, I have limited confidence that will result in a well mannered machine, without a great deal of luck. I hope I'm wrong about that.
Best regards,