Thanks for all the help and advice!
Dee - I'm going to remap the UV with the pieces not so close together and not so close to the edges.
Twinkle - I think I get what you mean. Place the base using the box tool, then use its coordinates as a guide to place the vertices for the back piece. Join the vertices together into a face (?plane?) and extrude upward. I'll give that a shot. I think that would solve my gap problem nicely.
AngelaMVeliza - I'm using Milkshape for everything, and I'm not finding the controls very user friendly. Also, the gap shows up prominently in the program you are using whereas it's barely noticeable in Milkshape's 3D view. Are you using Wings? I might have to give that a shot...
And here is my .wrk file - http://www.mediafire.com/?a9133bw68fx4tiz I hope the feedback so far is going to solve my issues though. I'll post again if I'm still having problems.