On a stock truck, if you exceed more than about 20psi, you will set an overboost code. If the MAP sensor goes bad, it can give erratic readings, causing this. Boost foolers that come with fueling boxes like TST PM3, just limit the amount of boost the ECM sees, stopping this issue from occuring.
Certain oils from air filters such as K&N have been known to destroy these sensors. This was a common issue here many years ago, but I really have not seen this in a long time. It could be the sensor has just died, you can try cleaning with throttle body cleaner or replacing the sensor to see if the issue goes away (assuming you are really not exceeding the amount of boost that the ECM is programmed to handle).
If you are exceeding the limit of boost, you can do two things, 1, get a boost fooler, or check why you are getting excessive boost. The stock HY or HX turbos (I think the 99s all had HY-35 w12cm housings, I can't remember) become inefficient around 35psi (just make more heat beyond that and do not move enough air). If you are staying below that, then you are fine. You will not damage the engine with that low of a pressure. The stock head bolts will hold 50+psi with out an issue.
If it is a stuck wastegate, it can be fixed, but it depends on the type of turbo you have (the HY and HX are different). A quick search here should find what you need depending on the model of turbo you have.