well at this point i recommend thinking if you really are hooked on THIS truck I had exactly the same experience as you as far as hearing a knock and all that. having traveled down that road and resolved the issue after a few thousand dollars, I should have gotten rid of the truck and bought a camaro or something. I'm sure that statement will be wildly unpopular but You should think about how big an investment this might become. with that said:
top end performance has real solid rebuilt engines from stock to full race builds, their prices are a bit high but they have a good reputation in the 2.6 engine world. I also would look into doing it yourself, if you can find a good machine shop a full rebuild kit is available for a bout 400 bucks. I built mine in about a day,(being as picky as possible) You also then can claim built not bought status
any way good luck man keep us posted