Next property was an unexpected $5,500 for a furnace and duct work.

If you get a quote on the roof and the comps support your purchase price + the repairs with a little bit more wiggle room in the budget for an unexpected repair or expense then your deal is likely a good start.

Depreciation also affects the book value of your asset and your equity as well.Also, your accountant will be delighted to see everything in one place comes tax season. 

You are already at the top of your budget, even if the seller agree to reduce the price, do you have budget for unexpected stuff you find during your repair?  

Finally, expect the unexpected. 

Obviously many costs are unexpected and can be difficult to quantify. 

Or a significant expense unexpectedly pops up (it will happen).

We had some unexpected issues pop up during the rehab that cost us money.

On a side note just to add some perspective - there's a decent chance you're going to run into 10k in unexpected costs within the first couple years of ownership, and that's part of the business. 

Many investors waive the inspection contingency, but keep the financing contingency, which is flexible enough to get out of the contract in case something unexpected is discovered.