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P0254 is fuel injector pump fuel valve current too high.
P1688 is internal injector pump failure.
P1689 sets when the ECM cannot communicate with the injector pump module.
P0217 sets when the ECM derates engine power to bring engine temperature down when it's overheating.
Three of the codes you have set are a cut and dry internal failure of the injector pump. It's definitely going to need to be replaced, but the transfer pump is going to be ok. If you've already had it relocated to the fuel tank by your dealer then it won't need to be replaced now.
The P0217 is a pretty common code that sets and is found when reading codes for other problems. If you aren't noticing any overheating problems I woudln't worry about it.
I have to wonder if they know this truck has already been converted to the in tank pump. It's not uncommon for the block mounted pumps to fail and take out the injector pump (setting a P0216), but the in tank pumps don't have this problem. I highly doubt you need to replace the in tank pump, especially at 2 years old. Make sure they check fuel volume from the pump before going through the expense of replacing it, I don't think you need it.
These codes all point to an electrical failure in the pump module, mounted on top the injector pump. Starving the pump of fuel because of a failed transfer pump can't cause any of these codes to set anyway. I don't expect replacing the transfer pump to change anything, even if it's found to be weak.
I'd bet that he didn't even look to see if the transfer pump is working or not. If he's ordered one he's assuming that it's still the original pump in it's original location and hasn't even done any testing, or he would have found that it's now in the tank. He's going to need to check for volume from the transfer pump, and if the pump is working then it's ok and don't let him replace it.
The pump should flow about 520 mL in 10 seconds of operation.
Either way if the transfer pump is good or not you are going to need to replace the injector pump. The three codes you have are internal electrical failures. The injector pump module that is mounted to the pump is part of the pump and is only serviced with it as an assembly.