3.8 Mommyvan off idle knocking...
Have you checked side play on all of the connecting rods? Endplay on the crankshaft?
There was a running change (around 04) where they made the timing chain THINNER by about 1/8" (cost reduction). This also required that the timing chain cover also was changed also to accomodate the extra thinner chain. To use the older (slightly thicker) timing chain, you would have to get an older timing chain cover to work with it, they are not interchangeable.
There was also a batch of thin wall blocks (they were 3.3L). When they were tightening the drain plugs on the blocks (one each side) with a pneumatic air gun, they would crack the block and fail the air test afterwards. They were able to get them through using an electric driver to run in the drain plugs. I would not recommend removing drain plugs on these blocks, instead remove a cup plug to drain the blocks. You may crack the block reinstalling the drain plugs if you remove them.
Also make sure you set the cam sensor in the timing chain cover correctly when you put the timing chain cover back on. It is very sensitive and cause it not to start if the gap is too big. They came new with a felt pad that would get knocked off by the cam sprocket. That felt pad was used to set the gap on the cam sensor and the felt pad would just fall into the oil pan.
Could your noise also be caused by the trans or suspension?