Well first off where there smoke there's fire. Disconnect your battery asap!!
Get under the dash and check the colum harness , even though it's new it could have a bad connector, that harness has a lot of load on it in a stock system .
If you had smoke the. Culprit should stand out like a burnt sore thumb
Also look at the back of the amp meter if you have one , those are a known fire waiting to happen
That peice is a noise filter capacitor it connects to the. + side of the coil then ground . It filters out noise from the electrical system so your radio doesn't pick it up.