Hello, I have an electrical problem that made rough idle on Chevy 350

Hello, we have 80 cutlass with 89' mr goodwrench gm 350 crate motor my son crossed battery cables and we seen smoke come from the starter area. The car started and ran ok right after but a couple of days after we started noticing it idling really rough and low. If you revved it up it would stall everytime coming back down in idle. As soon as I took the positive cable of battery it stalled so I figured the altenator was shot. But it does start first crank and runs still. The odd backfire pop too. Bought new altenator installed it. Now I can take battery cable off and it wont stall but still runs very low barely running. We also changed the fusible link on the selonoid. Almost seems like grounding probs? Out of the three wires there is big one going to batt. And one that had fusible link(which changed) and other red with a little white cylinder type connection on it that all goes to same bolt. The alten. Is working and sending power to batt. Not sure if its from recently crossing the wires or something else, but pretty much started happening after we seen the smoke. What else should I look for that would fail when crossing terminal cables? Cant see any burnt wires going to starter either