I do, however, own a 2 SFR buy-and-hold rental portfolio in Birmingham with plans to continue investing down there.

There has been more published, and the laws will continue to develop. 

If they don't complete the contract you resell and continue to generate more income. 

They spent $40k on renovations I'm assuming the driveway and garage played a huge role here.

You can drive yourself crazy trying to play  house detective on old homes. 

He said there is a high chance I'll have to continually clear the lines because tree roots will constantly grow into it, and because the line is made from old clay tile.

It’s hard to be both, and you’ll want to play to your strengths.Go all in, and prepare yourself to ride out the storms.Best of luck!

In my market the cost of a general contractor willing to play ball with 203k is such that BRRRR will not work since you will not have sufficient equity after financing the cost of said general contractor. 

My biggest questions are:Should the 12 rentals continue to be kept under a trust?

You should try, maybe you get a commission... but the big brokers don't play this game.