Plugs black on #1 and #2 cylinder (running rich) but not on 3 and 4. '82 Yamaha xj 550?

The bike has been fit with K+N pod air filters, Mac 4 into 1 exhaust and rejetted from 112.5 mains to 125. This was done at a cycle shop that specializes in old Japanese bikes and race bikes. They are well known, well accredited, and definitely good mechanics but anybody can overlook something. Especially if they are swamped. Or they might not have had the time to really test ride the bike.

The bike runs phenominally for the first 10-15 miles of the day. The modifications have added an incredible boost in performance. However, after 15 or so miles, the bike feels like it is either flooding as I ride or running very lean. It sputters, the throttle response is really bad, and it runs poorly.
If I am idling it seems fine. Low to mid range is bad. High range is incredibly good.

I did a few plug chops starting out with brand new plugs. Withing the first few miles the plugs on the #1 and #2 cylinder are as black as midnight. The plugs on 3 and 4 are getting black but nowhere near what I am seeing on 1 and 2. It can't be the coils as that configuration doesnt add up (1 coil for #1 and #4 and the other coil for #2 and #3 cylinder) If it was the jetting it would be even across the board (unless someone forgot to rejet the 3 and 4 cyl. which is incredibly unlikely)
I am wondering if they are out of synch and the new guy they have is the guy who synched the carbs. In that case, he may be unaware of the YICS shutoff tool that is absolutely necessary when balancing carbs on the YICS yamaha engines. But that wouldn't explain it. Not really.
It almost seems like there is a possibility that the 1 and 2 carbs were synched and the 3 and 4 carbs were synched. But the two side weren't synched together.

So this is where I am at but I don't know if i would get this problem with a bad synching.
Any ideas anyone?
 
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