Hold on a second. You have a business requirement that is met by the technology, but you aren't going to use it, because users refuse to pay attention. I don't think that's the right approach. You don't just assume Joe is going to go to lunch and not check in his file. You set a mandate that he MUST check in his file in order for the process to complete on time, otherwise they will all fail. That's training, and it is absolutely required any time you are using SharePoint at an organization, especially one where such 'checklists' are so critical (based on how you have written this). They must absolutely know how the process works, know how to check out, how to check in, and understand that if they don't check it in, then they are screwing over the entire business (or team or whoever is involved in this process). Catering to ignorance is not a best practice, so unless we're talking about senior executives in the golden years, I would suggest embarking upon a training regimen that shows people _exactly_ how document management is supposed to work and what is expected of them. Otherwise, you're going to have a non-working system. Just my opinion...
I don't know of any auto-save option or feature, but that once again is very basic training. You tell people how the system works and what they must do. They must save the form periodically within the pre-set session timeout limit in Central Admin (defaults to 60 minutes for a browser-enabled form), and they must know that when they are done, they must save AND check in the file in order for others to use it. While checked out, they must know that no one else can work on it, but since they can see who it is checked out to, they can contact that person to get an ETA on completion and/or to make sure that person isn't "at lunch."