One of the red flags that came out of that inspection was a note that we should have the brickwork inspected by a mason for tuck pointing.

This is a live and learn game and I love that you are willing to get right back on the horse when most people would tuck their tail and run.Win or Learn!

That I should expect appraisal and similar fees with others tucked into loan.

They may have a lot of unusual expenses tucked into their P&L - car payments, cell phones, travel, etc.You may add depreciation in your analysis spreadsheet below cash flow line  (NOI less debt service) to estimate taxable income. 

I have some money tucked away in money markets and 401k (50-60k).

Simple tuck pointing would be good inexpensive maintenance.

If you have a potential rental income of $2000/mo and a PITI of $1200/mo, that already shows that the numbers won't fit within the 50% rule... however looking deeper, I usually use the following numbers as an estimated budget:10% of gross rents for maintenance (keep this money tucked away until you need to make repairs)5% of gross rents for capital expenditures (I usually recommend 10% if the building is 50+ years old or has not been updated for a long time)10% of gross rents for management OR for vacancy (If you have a professional property manager hired, they should have a tenant lined up by the time your current tenant chooses to leave, effectively meaning you'll have a vacancy rate of 0%. 

However after a drive by this place is good area but tucked away on a back road that is horrible.

Have some savings for these items before you buy and then tuck away some funds from your rents each month to account for those expenses. 

I typically only do value add deals where I am taking on someone else's mismanaged building, so the up front CapEx can be pretty heavy with the new roofs, tuck pointing, electrical upgrades, window upgrades, etc.