We have seen our fees increase significantly over the last 4 years with Hall CPA (Brandon Hall's company). 

Hi Staci,If you don't have any plans on working as an agent for other clients, I would recommend a flat-fee broker with no commission split.

You need to develop a Scope Of Work that is precise and then start getting prices for all the work.Once you have that magic number, then you will add that to the cost you pay for the house, along with any other fees or expenses...Then look at finished Comps (get a Realtor like @Chris Ayars said) and see if you will make any money......

This is a little detail our title company missed...We contracted a lawyer after incurring close to $60k in engineering fees (they did find a way to lift the restrictions through the DEQ), to see if we could make a claim agains the title insurance.

Additionally, you will now have 3 houses (your primary and 2 rentals) that are appreciating, which is where real wealth comes from, not from the cash flow.

However, it hurts thinking about giving up over 30% of my 401k to fees and taxes.

I am actively saving for the next place, and would like to avoid the traditional agents, bank fees, etc, and work directly with the seller off market on my next deal. 

My bare minimum fee just to keep my license is 150/month to my firm, and that's literally just to be alive. 

So my question is, are there any creative ways to make this work for everyone so they can generate their cash flow free and clear while I am able to have a better cash on cash return and have additional capital to deploy later?

Not only will this add no additional protection, it will merely add operational costs.