Hi,
I've just stripped and cleaned a set of carbs off a FZR 400 (3EN1) and this has exactly the same carbs as the 600 3HE. The only differences were the size of the jets and that the 400 slide had much wider holes. These were not a DIY mod but made that way, so maybe your slides have been drilled or have come from a 400. If you look at the top of the slide where the diaphragm sits you can see where the two outer holes come through and around them at that point is a recessed hole. The recessed holes on the 400 were clearly moulded to accomodate the wider slide holes.
There seems to be a lot of discussion on the pros and cons of drilling slides but I don't think it would cause the issues that you have.
I have measured the 600 slides for you and the holes are 1.75mm. I can't measure the 400's because I just put the carbs back on the bike this afternoon. Here's a comparison pic that may help
I also found that three of my diaphragms had identical marks on them which had weakened and caused tiny tears. This had not noticably effected my bikes performance but they were very small tears, I was stripping the carbs due to an idle issue and rich running (confirmed by checking the spark plugs).
I did look around on the internet though and a torn diaphragm can be a cause of lost top end. I'd at least take the air filter off and operate the slides with a finger to check their operation. Best to strip the carbs check the diaphragms by eye, check float heights and all the rubber seals (the seals that hold the float arms into the body can shrink and leak too much fuel into the chamber, two of mine were way too loose). Do a bench synch and set the idle mixture screws.
Good luck with it.