My Mustang 2001 V6 3.8 won't start anymore.

History:
Couple days ago, I drove it with the low fuel light on, I knew I need fuel, but I thought I could make it. It did make it.
After couple hour, when I tried to start it, it cranked just fine, but did not start. I thought may be because of no gas. So I put three gallons of gas, and still could not start.
Problem:
I towed to a workshop, they replaced the fuel pump, no luck, still won't start.
By the way, the anti theft alarm light kept on flashing, so they disconnected it, and still no luck.
It does start when they spray some fuel thing ( I don't know where but in a tube under the hood).
When they checked the fuel pressure, no fuel coming there.
The fuel shot off switch is fine.
They did check the fuse and they are also fine.
No they tell me, may be because of the ignition key, but if it was because of the key, would it have started when they sprayed the thing???
They checked the injector and that is also working.
So what could be the problem?
This car had no history of problem, this is the first time, I am having problem. There was no accident nothing. Can you guide me what could be a problem???
By the way, they just made a new key with the programming, of course, and still no luck