My pro forma using the 50% rule and using standard expense percentages for San Diego both created a small negative cashflow.

Nathan G is right, please review the contract as every property management company determines what they are up charging or if they just have a percentage.

So in essence I think it is a classification error, you base your property's sale price on other sales in your market, however a percentage of the price of these other sales is due to considerations that your property simply does not have. 

Small percentage were just fine.

So on the expensive properties, the percentage will be far lower than on cheap properties. 

How do I calculate profit with Real Estate Commission Fees (Do I just multiply the 0.06% percentage to the ARV/MaximumOfferAllowed?)

As far as a 506B goes are there any syndication's you would recommend or better put, is there a online directory of available syndication's and their corresponding annual return percentages and projections out there that you know off hand? 

In my opinion, for one the companies that make the largest percentage of the stock market (Apple, Microsoft, Amazon etc) are currently thriving and this will continue.I know a lot of people lost a lot of money in 08-09 but that is likely because they were speculating or sold when they should have held.To counter your points I know investors who rode that recession through and lost zero money.

You may wan to talk to your CPA to make sure you have the same ownership percentage in both the active business and the rental activity that rents to the business and each are formed as either a proprietorship, S corporation, or single member llc.  

It has some fantastic reporting for repairs (broken down by the specific category), CapEx (including date placed in service and useful life tracking), and occupancy percentages.