I am looking for some insight into modeling a heterodimeric complex
in a single species.
...
The final structure looks ok visually. The DOPE score per residue
actually decreased by about .01 for a few regions between the
crystallographically solved structure and final homology model.
Otherwise is looks about the same.
Your procedure sounds fine to me. With that high a sequence identity,
your alignment is probably correct (and I'm not surprised that the
models look pretty similar). Otherwise the usual considerations apply
(e.g. you may need to look at sidechain packing if you're trying to dock
a ligand somewhere, etc.)