Doing my first cash out refi. 3.875% 30yr lower fees.Question how long should underwriting take?

Although their purchases are usually lower, so yes, we should see an impact, but I think it will be more due to uncertainty and not actually being denied. 

Like Non-Standard Rental Provisions, smoke and carbon monoxide agreement, etc. 

I got a pretty good rate (much lower than typical HML).

You have negative cash flow (which is normal while House Hacking).To improve the deal you would need to have a lower purchase price and/or be able to increase rents.

Correct me if I understood your suggestion wrong .. 1) Refinance the TH, which I currently reside in (primary home with 4.75) to lower the interest rate. 2 )  Do HELOC on the first SFH  ... here when I do HELOC, am I able to switch it to 30 year amortization same time (I need to refinance this place as well to increase the cash flow) or I have to do cash out refinance instead of HELOC?

I would approach that from the standpoint of the more I put down, the lower the monthly payment would be since it reduces the amount financed.

Since the values are high, your return cap rate will be lower. 

Top floor people should be considerate but don't hear lower neighbors.

Real estate prices along the wasatch front were too high to make sense and prices are lower in the basin.