One of the things the city is allowing is to defer up to half of permit and impact fees till final inspection, so at least if I will save some up front money. 

Permits, zoning, lot allotment, etc are all things you are possibly facing in this deal.

In regards to flipping, at what part of the purchase process should you start looking to pull permits.

dont listen to a plumber about a chimney where the water heater vents,the easiest way to find out if it is working properly is buy a permit and have the local building inspector come out and check the vent to make sure it is working properly if not then correct the problem my guess is, if the building is old and has been working properly for years it probably still willyou cant afford not to know for sure to cover yourself especially with a vent on a water heatergood luck 

I am going to assume that you have obtained the proper permits.

Site work, permits, land costs, utility connections, etc.  

City inspectors become familiar with all of us over time, so them shutting down a job after we have done a number of rehabs is unlikely so long as we pull the proper permitting.  

I have talked to a number of realtors in my area and these are selling well.Purchase lot $31,000Plumbing $15,200Electrical $10,600Concrete $15,800Dry Wall $12,760Flooring $4,000HVAC $16,158Lumber and cabinet package $66,976Driveway $3,200Landscaping $1,200Realtor fees when selling $13,000Bank fees and interest $4,100Building permit $1,700Labor to build - Paid to my construction company $36,750Total cost $234,344Going with recent history of what others are selling for in the area it looks like it should sell for a minimum of $250,000 possibly closer to $265,000.

I will probably be a the meeting on Wednesday (job permitting), so I hope to see you. 

Too many unexpected things pop up on rehabs that will set you behind - unexpected work, permits, or contractors not finishing on time.