Here's a guide:
1.) Browse .ipsw first (add 2.0 firmware)
2.) Click ispw builder
a.) Check Cydia / Youtube activation
b.) Add custom images if you have them
c.) I don't know about payloads
d.) Check what you want
Active phone
Wipe everything
Baseband Updater
Neuter Bootloader
Downgrade 3.9
Unlock
Auto delete
e.) Add bootloaders from Here:
Bootloaders

3.) Click build ispw
4.) Whe thats finished click iPwner
5.) Enter DFU mode, Here's how
6.) Restore new custom firmware in iTunes by holding shift and clicking restore