Carb Synchronization

[PepNYC]

I know there's about a million posts here on carb synchronization but I've checked the other posts and I can't seem to find an answer to this question. I just took apart and cleaned my friend's carbs on his 1993 XJ600 Seca II, from top to bottom. Needles, seats all the seals and gaskets, floats, jets, pilot screws, etc... I put the carbs back together according the factory specs in the Haynes manual. Put them back on the bike, started right up. Got my sync gauges out, synced 1 & 2, then 3&4, then bank 1 to bank 2 by syncing 2 & 3. 1 & 2 synced fine, 3 & 4 synced fine. 2 & 3 were not even close and I couldn't get them close. I'm not sure what could be causing it. She also idles kinda rough but I think its the mixture screws. I may have set them too lean. Did 2 turns out. I've heard 2 or 2 and a half so I figured I'd try 2 to start. Not sure that has anything to do with it but I figured I'd mentioned it. If anyone has any hints, tips, comments, or whatever or if I left any crucial information out let me know. Thanks guys.