I worry about checking the title, find it is clear of junior liens and then some loan company or attorney records something I can't get out of just before the auction. 

It really would be best it seems to get some professional CPA advice to clarify if any deductions were missed and to be clear on your full tax situation from someone who's familiar with real estate investing, as well as taking a closer look at what was (from your records) an ordinary repair/expense vs a capital improvement.

There are services that have low minimums of as few as 6 records for skipping at a time and even have a referral program so you can earn credits for referring others.

The six-county region’s median home price increased 20.2% year-over-year to a record $655,000, That’s $25,000 more than the previous median price record set in March.

My costs for this refinance are contract, notary, and recording,  it would be via the same owner finance lender (family) I expect this would cost me maybe $500-$1000. 

They're helping to attract the capital through their track record and you're helping to help them leverage their time. 

I have obtained a database of 1.5m records of MLS data of closed properties in my metro area.

@Todd PultzAs a City Planner in CA for 25 years, I can say with confidence that you were probably victim of a “taking” by the City not allowing you to build on legal lots of record.

I've seen a good number of discrepenacies between appraisals and county records (although it's always been less than 100 sq. ft.).

As long as the proper forms are filed/ recorded, agency is disclosed, and no one feels some shadyness is going around, you are good.2.