Fixing up an '85 FZ 750

Hi everyone

I wasn't sure if I should post this in the Technical section or Other section so moderators if you see fit go ahead and move this if you wish. I am fixing up a friends' vintage Yamaha FZ 750. Issues it had were:
Leaking fork seal - fixed.
stalling when hot and near impossible restart - found out the valve clearances were way to tight - reshimmed and adjust all 20 valves to spec.
Cleaned carbs and replaced needles and seats in all. All jets and passageways cleared. Vacuum diaphragms all good and function well. Float levels are set dynamically with clear tube to indicate actual fuel level, as far as I can tell it is within spec of 8.3 mm below lines of float bowls.
At least now the bike does not die when it heats up and seems to restart ok, but it really has a hesitation issue at 2500 - 3000 rpm at any throttle opening. It seems it can't get out of it's own way until you drop a gear and get up over 3k then takes off and runs like a Banshee, and fuelling feels just fine up at higher revs. It has a Vance & Hines 4 into 1 aftermarket exhaust and I am sure that is not helping. Idle mixture screw are currently at 2 1/2 turns out, idle is quite lumpy with popping in exhaust on decel. I tried dropping the needle clips down from center to lowest notch, and this did nothing to help, so I returned them to the stock center position. As far as I can read the jetting numbers in carbs are stock jets, and it pulls so hard at high revs that I think at least the mains are spot on. It just seems to be low speed anything below 3k that it sputters and really makes in-town riding a chore. I did a leak down test of all cylinders when I did the valves and they all show less than 8% leakage so pretty sure no mechanical issues. I'm pretty sure there is no vacuum leaks around carb boots = sprayed with brake clean all around no change in idle. I had a better idle with the idle screws out 5 1/2 turns but went up a mountain road and it would hardly stay running when I stopped so must have been way too rich. I also synced the carbs numerous times and am confident they are all even across the board. Also new spark plugs put in. I'm getting real tires of these carbs real fast, can someone help me out?

Anyone?

How did the plugs look? With stock jets and a V&H exhaust along with the popping on decel you described it sounds like it's running lean. Any residue inside the exhaust tip? But I'm a carpenter not a mechanic........:

Plugs looked not too bad when pulled but where very worn so hence the replacment. Inside exhaust tip is kinda sooty so maybe rich? I backed out the idle mixture screws a 1/2 turn and the popping on decel has improved. I tried moving the float levels up and down about 1 mm and it made absolutely no difference to the dead zone from 2-3k rpm. It runs so strong and clean above that however. I'm starting to wonder if it always ran this way as the owner bought the bike like this and never modified anything. Was reading somewhere that possible the V&H exhaust having larger headers for good top end does not present enough backpressure at low rpm for the carbs to fuel properly? Something about putting a venturi in the collector? When it is in the dead zone the engine will not pull out of it - the more throttle I give the worse the misfire and hesitation gets. Almost make me think about a weak coil (s) as this may be the speed where cylinder pressures are highest and demand the most voltage to fire the plugs? I wish I knew if this is spark related or fuel related, as I am almost sure now that it may not be carb related as any adjustment to them seem to do nothing for the dead spot, they do however affect other areas. If I back out of throttle just enough and there is a slight downhill the engine will slowly pull through and then get along and pull hard.

I had a friend who had an 89' FZR 1000 and put on a full D&D system - his bike originally had EXUP. That thing fell flat on its face below 3500 then got downright violent, wish I was more knowledgable on the black science of carburation

Yes that exactly describes this - after it gets out of the fall on face spot, it gets downright violent!!