If the battery charger had smoke coming out of it then I would not recommend using it again. The OEM Currie battery charger that you purchased is a high quality charger and was tested by us before we shipped it so chances are that there is a short circuit somewhere is the wiring harness (possibly caused by the old charger plug breaking inside of the old charger port and causing a short circuit that fused two of the wiring harness wires together), or caused by the new charger port plug being wired in reverse polarity to the wiring harness.
The first thing I would check is the new charger port's connector where it connects to the bike's wiring harness. The wiring harness red wire should match up with the charger port red wire. If the wiring harness red wire matches up to the charger port black wire then that is the problem.
If the charger port wires match the colors of the wiring harness wires where they plug together then I would inspect the wiring harness for any signs of damage or burning, especially in the area where the plug that connects to the charger port attaches to the harness.
Please let me know how it goes.