> to do R&D themselves that the software team can then refactor and ship to production
What academics produce is most likely proof of concept or a prototype, not something you can "refactor" and ship. It's not a matter of tooling and programming languages, but of what is actually produced. Software engineers produce software that meets all sorts of non-functional requirements, experts care about functional side only. So get all sides to agree on what will be produced and then ask developers about how they will proceed with putting that in production. It may require redoing most or even everything.
> They also don't seem to have a big sense of the urgency needed at my small company.
You don't do creative work to a schedule, especially urgent one. The only thing you can predict reliably are the ones you have already did (and only if the circumstances don't change). People promised self-driving cars long time ago, and we still don't have them, regardless of any company sense of urgency. You deal with that issue by discussing stages and scope of delivery with all sides, not by expecting their understanding of urgency.
> It doesn't seem like they should be treated as a separate team because too much will get lost in translation
That's true, getting managers to act as translators between experts and technicians is a really bad idea.
> How do I set timelines when it's hard to understand the work?
You ask them to set them for themselves. You don't need to understand the details, you need to understand what will be produced and how all involved sides will use it and that they all agree here.
> Should they integrate with software best practices or just be their own thing throwing successful R&D over the wall?
That depends, but most likely you will have more success passing what they do to your developers (who are great at being software developers) than by teaching software development to someone who doesn't understand it. Some training may be beneficial though (so that their work can be used by developers).