I cannot think of a way that you (the LL who stands to "benefit" by them repairing their own space that they are paying you to use) will come across in a positive way.Plus, the tenant who incurred damage due to the other tenant's leak, may have some legal rights to have the tenant with the leaking pipes pay for the repair in both spaces.Now, beyond the legal side, you also need cognizant that most mom and pop tenants (which I assume these are) are not great with their money.  

Please note, I did not include the tax benefits from deprecation.

Great post it gives insight to how you worked the systems and benefited.

It takes a lot of work to find a tenant, your commision gained from the income should only be for the services rendered while the tenant is in the home ( in my opinion ).Some additional fees I can think off, are maintenances fees, for larger projects that require a lot of management and research.

Even though you feel you don't reach the full cash flow potential, you gain on making the lives of those families more comfortable.

Most I know fully disclose what they’re doing, the risks to the homeowner as well as the benefits, and will actually tell the homeowner id\f they think the homeowner has a better option.  

I am going to get hit with capital gains and state taxes(Idaho 5.8%)..closing on cabin on the 18th of Nov.

This doesn’t make it a bad deal, it just means giving up something for a  different benefit.  

How much and what would I do with the gain on sale, and how does that help or hurt my strategy? 

You are in a great spot to re-start your journey, especially with the help of your VA benefits and service to your country.