Thanks to all who contributed to the discussion on solving the problem with the COMPARE scripts. I deleted the extra chains, etc from the xray PDB and then renumbered the residues so that they matched with the MODEL pdb. This solved the problem when comparing the model and the actual structures. But when I tried to add the template to the comparison (just like they do in the example script) along with reading in the alignment file, MODELLER complains. The error seems to be with the MODEL and xray pdb, not the template... that seems weird since it was successful without the template or the alignment file. I'll look into it some more.
Again thanks for the responses.