HVAC quote too low?

[John Vietmeyer]

I'm renovating a 1970s 1600 sq foot rambler that needs all new duct work in crawl space and a 3 ton package unit.  Quotes were $12,000, $8,500 and $5,300.  I know and trust the companies on the first two quotes.  The $5,300 quote is a guy refered by my floor and paint contractor.  

The variables I think I need to consider are:

1) use of metal vs flex duct

2) type of unit installed and warranty

3) will permits be pulled / work done by licensed professional

I want to save money but don't want to create headaches. If I can save money On the HVAC, I will be able to invest more in renovating the kitchen.  Any thoughts?