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I recently made the move from N52 --> N54 and went through the same thing, reading a lot of forum posts where many of them are a well over a decade old. Most of the maintenance related posts are fine but a majority of the performance related posts are horribly outdated.
For example, the decision between JB4 and MHD. JB was awesome back in the day when the DME was locked, but theres virtually no need for it any more. Some folks are using them for methanol, but realistically if you're picking one thing to do in 2023 there's nothing easier than MHD. Cheaper, faster to install, easier to install, and easily reversible. I actually just flashed it on my car today and I'm very pleased. Even the stage 1 tune for trash CA 91 octane is a very noticeable increase over stock power levels.
Also MHD will give you details of any error codes you're having including that half engine light. My guess is that it's a 30FF boost error. You said the vacuum lines to the waste gates were replaced, do you know if it was just the short pieces from the boost solenoids to the wastegates? If so, there are a lot more vacuum lines that could be cracked. MHD also has a software-based wastegate rattle fix that you can try.
As for intakes and downpipes, you shouldn't worry much about that yet. The OEM air box is plenty sufficient for big power on the stock turbos. DCIs let you hear the turbo sounds and barely improve performance if at all. Catless downpipes are cool if you live in a place that doesn't have emissions inspections, but even then you should prioritize maintenance and suspension above all that.
You didn't mention the state of your plugs and coils. These engines are rough on spark plugs compared to the N52 so if you don't have any history of having them replaced recently you should look into that. Some say replace coils too, but I personally run them until they fail.
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