Permits and Inspections

[Pavan Krishna]

When you get work done on your homes, do you make the contractors apply for permits? In the past, I had issues with contractors doing
substandard work. For example once a HVAC was installed without an air filter.

Now, due to some rodent problem, I need to replace the ducts in one of the homes. I asked the contractor to apply for permit and inspection. He is charging me $1,250 extra for the permit process. They "guarantee" passing inspection (for what its worth). He is asking me to pay in full, as permit process can take months. My questions are two fold:

1) Should I pay in full (including $1,250 for the permit) when the ducts are replaced? Even though inspections were not complete.
2) Once I pay in full, if the contractor never applied for permit or inspection has issues, how can i make the contractor hold their end of
the bargain?

Any thoughts are welcome.