Im in the middle of shortening the wires on my battery. I cut one of my wires too short I can still make it work with what I have. Will it effect the battery if one of the wires is longer than the other? The wire that is shorter is the positive.

Nope, won't affect the battery in the least bit.

Great thanks

Only a suggestion, but you may want to consider making the other wire shorter too. Having one wire longer than the other won't hurt a thing...but as you flex the wires/connectors around in your chassis, the different length wires could cause some binding on your solder connections and eventually weaken them or worse.