However, in California, each LLC incurs an $800 annual franchise tax plus gross receipts fees if revenue exceeds $250,000, and property insurance may cost more.

Fixed Mortgage does come with closing costs and points upfront which the HELOC does not, except a $95 annual fee. 

I have the ability to find properties that all in costs including rehab and purchase would only be 70 to 80% or ARV on properties. due to this I have been trying to find lenders that allow for less down and rehab coverage since the properties are so discounted.

Although the list may seem intensive, I look at it like this: The total cost of all these items can be much lower than the cost to repair a hidden surprise after purchasing a property to flip. 

The forms are online, and it costs $100 per filing. 

If they tenant is $300 below market, that's costing you $3,600 a year.

A CPA who specializes in partnership issues can also likely talk through these issues with you.3) Depending on the size of the deal - Keep It Simple - the number of really complex agreements that come across my desk for a $500k property is crazy, and it ends up costing as much to do those tax returns as a comparable $5m deal

Don't know how to analyze a deal effectively?

If you've dealt with this how much did it cost and how much time did it take to resolve it?

Quote from @Patricia Steiner: There are several lenders who offer low/no closing cost options for first time homebuyers.