I am in the same boat. I had to install 3.1.3 on my BIL's 3GS and JB with Spirit since my Mac did not let me install Pwned 3.1.3. He bought his 3GS the day it was released, so I assumed he has the old bootrom. I have the SHSHs for 3.1.3 saved now.
I was getting 1600 and 1603 messages when I tried to use Pwnage with 3.1.3 and I think my mistake was having Pwnage in the Applications folder and the 3.1.3 firmware on the Desktop. I wanna try the procedure again so that I can try to put 4.0 on his 3GS.
Looking at various things, can I not follow
these instructions to JB with Pwnage tool on 3.1.3 again since step 8 specifically asks if you have pwned before and if you don't drops the payload on it?
This was I can use Pwnage again to JB 4.0.