I'm trying to do a comparative analysis of a gene cluster in homo sapiens with other species to do inference on evolutionary traits.

In species that are close to homo sapiens and have high quality sequences available at NCBI/ensembl I can just look at the flanking genes and download the data BUT in species that are not closely related or have poor quality sequences I need to download data from several scaffolds.

I know I can, for instance, download every gene's orthologues from ensembl but I'm thinking I would like to get the scaffolds containing them so I can do a more robust analysis.

1. Should I go and try to download the scaffolds containing orthologues?
2. If 1, what is a good way to do this?

Thanks in advanced, this is my first question and I hope it is not too vague :)