We get our money from longer-term Wall Street investors, so our rates are tied to the bond market, particularly the Treasury (watch the 10-Year Treasury...rates will move in that direction).

My financial advisor scolded me for buying another house and said I should go for non-RE investments (bonds and index funds). 

A termite treatment and bond later and we were back in business.

This would leave you $30k to offset any capital gain and recapture tax.You can also use it to offset other "passive" income, but not earned income (unless you are a real estate professional), or portfolio income (stocks, bonds)I would check with a CPA to see if you qualify based on your income and profession, but you're probably good.

This is a fundamental to investing...whether in stocks, bonds, real estate.

Those require you to live in the property, and we have some great options like Oregon Bond (lower rate or down payment assistance) and FLEX (up to 5% down payment) available to Oregon residents. 

So the leap to do PML wasn't hard since I knew more about RE than stocks and bonds.

What are the pros and cons of using an entity to invest in other asset classes (i.e stocks, bonds, mutual funds) vs in your personal name and what are some deciding factors for you to help with that decision?

How you may proceed will be subject to state law, rights of priority, escrow or bond might be required, then again contingencies might not be required. 

The only thing I'd recommend is to removal all the hardware but make sure they stay matched up, ruff them up with sandpaper, clean them and do the first coat with bonding cabinet paint ( cure time is 24+ hours/ coat) then top with semi gloss.