2003 Honda Shadow ACE 750

My bike has been sitting for approx 1.5 years. I drianed all the bad gas from the tank and carbs/reserve/etc. I got a new battery and the bike kicks over and starts and runs poorly on one cylinder. It will not stay running and cuts off immediatley once choke is disengaged. When I first started the bike it ran on the front cylinder. After putting in the new gas the back cyclinder worked and the front cylinder stopped working.

I noticed that although the lights work and blinkers work but the fuel pump no longer cuts on when the key is turned so I think the pump is mostly responsible for the issue with the rough starts. My brother removed the fuel pump and tested it separately and it worked fine. It just doesn't work when hooked up to the bike. Anyone have a similar issue before? Any help would be greatly appreciated.