If you residence is allready in a commercial/business district, you don't need a "permit". A letter stating you are in complince with all zoning bylaws may help but isn't required.
Your order should be;
1. Check with CLEO to see if they are OK with you having gun shop. BATF&E site visit person WILL talk with your CLEO, even as late as the day of the site inspection.
2. Open business checking account and pay for everything through this.
3. Get town/city business license.
4. Send in BATF&E FFL application and all associated paperwork.
5. While waiting for ^, get your EIN number and Inc. or LLC paperwork ready.
6. Have BATF&E site visit. This should go smoothly as you have done all your homework and know all the answers to any questions they may ask.
7. Get FFL and have your PD put in for State licenses, Dealer, Ammo & gunsmith.
8. Get furniture, security, stock and initial cash to start shop with.
9. Receive state license/s.
10. Open.