Ya know, I actually did this myself the other night. Got on strobist, made the light box from a cardboard box, put down some plexiglass, and used a black posterboard for a seamless background. I also got that line in the back from the end of the glass. I don't see any way to really deal with it other than post processing it out of there. Someone smarter than me will hopefully step in now and say "Hey wait, here's how you deal with it...!"
I'm at work now, otherwise I would throw up some pics, but here's the link -
Strobist: How To: DIY $10 Macro Photo Studio
It worked REALLY well. Really surprisingly well. I did end up using kleenex instead of tracing paper b/c I couldn't find any, but it still was surprising.
One thing you might think of it picking up some color correction gel for the flash you have, and some halogen work lights. I haven't used them myself, but I've seen a lot of people who liked them and were on a budget.
Unfortunately, being next to a complete noob, I don't really have much in the way of critique, just hopefully some ideas you can use on equipment
Mel