Pyramid.....Are you to mean that not all the battery cells sit flush(flat) with the chassis? Or do they not fit into the slots at all?
If the calls are not flat, you may need to resolder the batteries so that they are flat(using a jig of some sort) If the cells cannot fit into the slots, you may need to file the openings a bit more to accomidate the size of the cells you have. Dont forget to file the edges of the slots facing the batteries at approx. 45deg.
If all else fails, you could build your saddle packs in the chassis. Granted you shouldnt need to go to this length, but... by placing the cells in the chassis first, taping them down and then soldering the bars on, you guarantee that your packs will match the slots. But again, you shouldnt have to do this(unless you're really anal about things of this nature).
Good luck
Gavin