One of the first principles of electrical troubleshooting is once you let the smoke out you can't get it back in. Smoke is usually an indication that something got fried. Check carefully everything; components, connections, wiring around the battery box and see if anything looks melted, discolored or otherwise suspicious.
You didn't mention if the new wiring has a fuse or fuses in the system. If so, did you pop a fuse?
If there are no fuses you will want to add at least a main fuse to your harness as you work through this.
And as mentioned, diagnosing with a multimeter will lead you to the source of your problem. Keep in mind though that the smoke episode may have "burned clear" the voltage path to ground. You may not now be able to find a direct short but you should be able to identify a failed component.