What are other ways I can get permits for mods other than filling out the form from the DoT? Those are expensive, you have to pre-pay about $100!!!

And what do people mean when they refer to, "the pits"?
Are there OTHER WAYS of getting permits for mods?
Also, what happens if I go to an inspection centre and they say that my modification is illegal... Will they defect my car and say that I can't drive it anymore from that moment?
Could someone tell me the process.