Was that carb ever laying on its side while you were doing the motor swap. If it was anything but horizontal (same as when its on the motor) at any time, you might have a float sticking issue in the carb.
I have an 87, and it has original lines on it (they need replaced this spring) but they cant be backwards my supply line crosses from the drivers side to the passenger side at the back of the motor, and the return continues up the drivers side to the shock tower, then turns upwards toward the filter.
'87 YJ, 4.2L built and bored, 8.5" of lift, 8.8 rear, AX15/NP 231, Tom Woods drive shafts, Flat fenders, 12,000LB winch, Custom bumpers, Rattle can paint job. Never completed...