So...am I shooting myself in the foot if I buy an investment property now (out of state) to begin my real estate career, and lose out on the ability to use an FHA in LA down the road?

Personally I have never been a fan of pre-tax accounts (401Ks and IRAs) because I feel like they constrain my ability to invest in the assets I want, so another consideration you may have is to temporarily stop those investments to save faster for your house.

Their ability to help you is limited if you go after. 

What impact does this have on the performance of your rental properties and your ability to invest in the next deal and grow?

The reality is that the tax impact and ability to take ANY losses (as Michael mentioned) is based on a number of factors that include whether or not it is a "separate dwelling unit".

If the leak is due to the software I would switch to a bigger more national brand instead of some company that is smaller and has the ability to have cyber issues.

Despite them performing inline with rent projections and occupancy, their flaw was in a short-term rate cap without any ability to refinance.

This can become a risk for both you and your ability to sell.As for things to talk to HOA about, beyond the permanent exterior colors/finishes, I would also ask about things like dumpsters and potentially port-o-let's that may be needed during rehab.  

Will they lose their ability to deduct bonus depreciation against their regular 9-5 income for all future years?

You could have sent him to collections and this would destroy his credit, which could impact his ability to purchase a home, qualify for a car loan, and possibly even cost him his job.