Pete 379 not starting please help

1999 Pete 379 3406e. Been at the spring shop getting work done for 2 weeks. They called me and said the battery's were dead 2 of the 4 battery's had dead cells. I kinda figured before it needed battery's cause they would smell like rotten eggs but anyway they changed battery's. Now the truck won't start. Cranks just fine just won't fire up.... runs if starter fluid applied. Getting fuel pressure at the filter. I did notice the amber engine light was blinking continuously. What does this mean? I can't even pull the codes when using the cruise switches. So now this truck is stuck in there shop and I'm not making money with it soo can someone please help a d tell me where to look

 

So a mechanic came today and couldn't get his laptop to connect to the ecm..... we swapped the ecm with one from another truck he had there and my truck fired right up! So I ordered a ecm this afternoon but can't ship out till Tuesday so hopefully comes in on Wednesday