If I compare the Schiller SFBayArea median home price vs S&P500/NASDAQ, the percentage increase since 2000 seems to be about the same.

They also use my brokers' license allowing us access to the MLS for retail selling of property and comparable information.

Since the account is a traditional and subject to tax, just wanted to make sure I am able to transfer within 60 days in order to avoid tax.Does it matter if I transfer into a new IRA account?

I don’t know about the specific property you are talking about, but my guess would be someone is using a HUD financing product that comes with a restriction that they have to rent to people below a certain standard compared to the median in their market.

For FHA I don't know but for a traditional loan why would it matter? 

They expect a smart borrower to shop around and compare terms, ask one lender if they'll match or beat another.

Initially my wife was pushing for the heloc as the method to get our down payment money but I insisted on as closely as possible comparing the numbers to the cash out refi. 

In a traditional GoE scenario, the house appraises for say 300k, they still owe 200k, and the GoE is 100k (which is used as a down payment on a 200k mortgage).

Traditionally, beach towns generate money and tourism due to the beach, if polution is such a large concern how would this impact IB?

Those are good places to start but you should always look for sales that are comparable in type, size, condition, and amenities.