If I know anything, it's that I/we are definitely NOT perfect and we can always do better.

I completely agree with the advice and I'm perfectly okay with not charging him rent.My concern is that by treating this property differently from all the other units in the Series LLC, I may be opening myself up to a situation where I'm weakening my LLC protections even if I keep the financials separate and in order.

Or any tips for mitigating risks when market timing doesn’t align perfectly?

That is as close as you can get to perfect alignment between GP and LP. 

My own garage fridge was my kitchen fridge 20 years ago and still works perfectly. 

Starting small with solid fundamentals and not waiting for the "perfect" deal was key to getting started.

I am not looking for the perfect deal, I just want something that will improve my financial position better than just dumping all my money in a high yield savings account or something.I don't need to live in the nicest place.

I am never looking for a sure thing as I don't really think they exist but I don't want to get into something that I am not sure how it will look in 3 or 5 years.The only way I would look at this deal is if it is perfect for getaways and relaxing for me and the family and anything I made would help pay for those experiences.

The basics of a seller financed deal are that the title co or closing attorney (if there is one) or seller’s attorney draws up the warranty deed transfers title, the promissory note evidencing the debt related to the transaction, and either the deed of trust or mortgage (whichever is being used) perfecting the lien against the subject property.  

It has helped considerably but isn’t perfect.