I'm just starting to get into the rental business and I'm trying to figure out what figures I should use for estimated repairs and cap expenses as a percentage of the rent or house price.

what do you use for a calculator to analyze and where do you come up with the percentages for the different fees 

So of the small amount of people who actually step up and do some profitable wholesaling it seems a high percentage of them quit soon after from burnout. 

When I enter estimated potential rental income for the top floor (2000) and 1st floor (1700) and a garage space I can rent for storage (100) my cash-on-cash percentage is in the negative (about 11%) and monthly cashflow is -$100.00.

You have to put down a percentage up front and you make payments on the loan like a mortgage. 

Maintenance is not a percentage of rent, but actual dollars, so the lower the rent, the higher the "percentage of rent".I would rerun your numbers using 50% for expenses, plus Mortgage, and then see what your cashflow is.

I would also likely take a percentage of every repair too, including the ones where the homeowner insisted on the contractor.

You need to keep shopping around because you are probably sitting high on their risk analysis for potential payouts. 

The total of those is somewhere in the neighborhood of roughly $12.5K, so after the penalty and additional 10% withholding I'm assuming the actual payout will be approx $10K.

I'm assuming there's a ballpark percentage...any input is greatly appreciated.