Ok first I am going to say I think some of the problems you are having stems from using a crown vic efi harness, I maybe wrong but those where non ho engines and the sd computer will be for ho, thus different firing orders, while this may not be a problem in itself it may be an issue with pin location. I will post a link to an old thread that may help, you have peaked my intrest in this because I'm thinking of an efi swap in a vintage body but I will be using a harness from a 91 stang. I already have the harness plus a spare one and related computer, look over the thread I linked and see if it will help you determine what problems you are encountering.
http://www.rowand.net/Shop/Tech/FordEFISwap.htm
I will be doing more research on this too so keep us posted, hope this helps.
http://www.rowand.net/Shop/Tech/FordEFISwap.htm
I will be doing more research on this too so keep us posted, hope this helps.