After replacing the alternator, the engine turns over slowly and backfires and will not fire?

Got into my car this afternoon and started my car only to find an error message stating that there is a problem with my charging system. So, I drove to Orielly auto and shut the car off and asked if they could test my alternator and they did. It was bad, so I shut the car off and got the price only when I came out of the store my car gave me a click and would not even try to start. So, I bought an alternator and while I was putting it in, I had jumper cables from my friend's car hooked to my battery and when I was done the car turns over slowly and backfires and will not necessarily fire. I'm not sure what's going on with it. I know it should be getting fuel because I hooked up the fuel pump to direct power so I know that can't be my issue and I'm very lost now and out of ideas. Can anyone please help me?