check the compression in each cylinder. if your above 100 psi in all of them and the lowest is within 20% of the highest and none of the cylinders takes a lot longer to come up to pressure than the rest, the engine is probaly ok. (make sure you don't have heavy oil or additives in the crankase when you do the test, you'll get false readings. use 10w30 or 5w30 for an accurate reading).
if everyting checks out ok with the test then i would replace the valve seals.
the knocking could be comming from a bad o2 sensor which gives too rich a mixture, mine went south and i thought a piston was going to come out through the side of the block, thump-thump-thump.
the test above is a general test for most engines, you might want to get more specific numbers for the 3.9
my 3.9 has 270,000 km on it and it's still good (i've use only synthetic oils in the 7 years i've owned it, a lot better in the colder weather and probably why it's still in one piece, yah i'm amazed too fox!)

oh by the way guys, HOW ABOUT THEM STEELERS, YAH BABY!

 

I'm not too sure about the overall longevity either, but my '92 with the 3.9L has just a tad short of 262k miles and all I have is a rocker that knocks on start up.

 

here is a search of the 200,000 mile club when i searched for 3.9L. there are multiple pages so hit next at the bottom. one has over 400,000 on original motor!

Link:
http://www.allpar.com/old/club/searc...9l&type=engine

 

that is insane. well its good to know my trucks got lots of life left being that i take care of it, which i do!