First, off, please, please, please keep this thread going, or turn this into a journal at some point. Mexico (probably Baja) is a retirement destination for me, and I'm sure others as well, and we would all love to hear your perspective and travails.
There's a large US expat community in Baja, especially in the larger centers like Mulege, Loreto, San Jose and Cabo, and the like. I would reach out to them (if you already haven't) about US/Mexican specifics and how they may affect your business and your partner. And as for your concern about ACH transfers raising eyebrows, your well-substantiated tax return should lower them immediately. You'll have to account for every dollar of your earnings to the IRS anyway. Lots of expats operating in Baja, and money wired from Mexico is not an issue. Finally, your bank or brokerage should be able to tell you if you can add your partner to the account.