It's absolutely normal for a centerline induction twin to run leaner and warmer on one cylinder. The crank interferes with equal fuel distribution. Unless you have a twin carb set up, where each carb feeds it's own cylinder, this won't change. Even piston port and throttle body fuel injection does similar. Only direct injection provides equal balance.

Put the engine back together the way it came, with wrist pins and bearings in the same holes and oriented the same way, and continue the break in. Don't get things hot, just middle of the road highs and lows. No lean tuning.