could down grade to ballasts designed for 2 bulbs. I haven't looked at the wiring in any of my t5's but the ballast should be getting source power but i know on mt TEK is runs a parallel circuit and if 1 bulb is missing another won't light up. but if that one bulb burns out power will still go through it to light up the other bulb. well i am bored and decided to have a little fun on ms paint, this is how the circuit is probably ran right now:
Now basically all your trying to do is remove 2 of the bulbs and that should be a diagram for each type of circuit that you plan on running. The one thing with this idea that if its a single series circuit you might get less resistance which your bulbs may give off more light. lol i don't know, kind of rambling here.
edit: crap forgot to label the box in the picture, thats your ballast