If we are living outside of the U.S., will my non-U.S. wife's business income be subject to Section 965 Transition Tax, Form 5471 and Self Employment Tax simply because I am married to her? What if I am employed by her company?
If she is no longer a US resident, then she should not be liable for US taxes.
My wife is a US citizen and I am not. She works for a company I own (more importantly, she owns less than 10% of it). She does not pay self-employment tax to the USA.
Let's start at the end: you should really talk to a tax professional before you make any decisions.
Your wife is a non-greed-card holding resident alien; she can become a nonresident alien once you move abroad, but even that isn't as intutitive as it seems. Once she is a nonresident alien, she may want to stop filing jointly with you, or maybe elect to contintue to do so - there are some benefits to that. Check out this, for starters.
The fact that you own a company and work for it doesn't mean you are self-employed. On the contrary - you are probably an employee; it's possible to be self employed under those circumstances if the company is treated as a partnership/LLC for US tax purposes, but that, too, isn't simple to determine.
Really, talk to a professional....