Bill shock

Any ever get a bill that was higher the expected or something the took longer then expected?
I drop off my truck today at the dealer to take a look in to why the truck is surging or loosing boost. The dealer was able to replicate it pretty easy. Boost would not go any further then 20psi. They started working on the truck since 7:30 am. I go there around 11:45am and ask what is taking so long and they say they are still looking in to it. Call me back around 1:45pm saying they want to preform a EGR test on it and I say ok. Call me back 15 min later said think they found the issue. The ECU that was swapped off my old engine (new one did not have it) was some how programed for pre-egr and it was dumping boost because of it. I ask how much to reprogram and he just said time.
It is now 5:00 pm. So far no update on anything.
They have now had the truck for 9.5 hour, I am sure there was some breaks in between.
Now I am thinking this will be a extremely high bill.

 

When I bought the truck it came with no warranty and it needed the engine rebuilt or swapped. I got a junk yard engine that was a reman with 220k on it. The truck was clear out in NC. I had a shop there swap it out, they told me the replacement engine did not come with a ECU so they took the one off the old one. So not sure how they could have screwed it up if they never hooked up a computer to it and just swaped it out. The only thing that was new was the VCU because that was stolen before I bought it. The dealer payed for that one.
I am trying to figure out way it was programmed like that. The EGR was not blocked off on the old engine and I am sure the low boost and surging was noticeable.

 

I am more mad they could not figure it out in less then 2 hours like the thing on the counter said they can do. That was the reason I took it to them so they could hook it up to a computer and figure out was wrong. I was unsure if was the turbo or the injectors. I did a pressure test on the main pump before giving it to them to make sure that was not the issue
Once they knew it was boost why they just did not check EGR then is beyond me. Soon as they told me about it I googled around to see how the waste gate worked on this turbo and came across EGR not closing being the number one reason for loose of boost.
Here is me being ignorant not not thinking right. 1. Some how it went around me that the EGR is tied to boost. 2. I thought it was always closed then opened under load not the other way around but if I would have looked at my old engine (it was wrapped taped up in a tarp so kinda hard to see) I would have saw it is always open. 3. I also did not think it worked while in neutral, only while driving.
The only thing I knew for sure was that the valve was not stuck after I tested it and I thought if something was wrong it give me a code. Well I can not have a code if the ECU knows nothing about it!
Here is the other thing I have had this truck for about 2 months now and only driven it from NC to IA. After that I had to do a lot of other work to it so it has not moved much since.