Cbr f3 fuel issue 1998 honda?

after having my bike sit for a year in a shed, I drained the tank and replaced the fuel filter. It ran great for a 1 1/2 days and then just randomly died. I finally realised today that when I drained the old fuel I sat the fuel tank and pinched the hose going into the fuel filter so there was a pinhole leak and the hose was bent so very little fuel was getting by. My question is, does it matter in what position the fuel pump sits in order for the bike to operate properly. There are two groovs for the fuel pump to sit horizontally but since I had to cut out part of the fuel hose I had to (at least for now) to position the fuel pump vertically. After I got the leak fixed I took the bike for a ride and it ran fine until I got pulled over, after I was done with the cops the bike wouldnt start, I ended up killing the battery. So again could the fact that the fuel pump sitting vertically instead of horizontally prevent the bike from starting or to run rough?