I have a 93 Dakota 3.9 with about 175,000 on it. Those engines are notorious for developing sloppy timing chains, which is probably the source of the rattling. As built, they don't have any kind of chain tensioner, however Mopar sells a mod kit that adds one. Mine made the rattling noise, and for the longest time I thought it was pinging due to the fact it started making the noise at a rather young age. Also, it kind of seemed as though the noise increased with throttle load, but that must have been my imagination. Finally, the water pump went out two years ago at Christmas time (at around 155,000 miles) so I decided I would bite the bullet and dig the rest of the way in and replace the chain as I had heard so much about what a problem area that was for the 3.9. I found it to be as loose as a goose! It hadn't jumped time yet, but it may have been getting close. (BTW - I propose the idea that possibly your's HAS jumped time, which may be the reason for the power characteristics you're experiencing.) Anyway, a new chain and gear set brought about a quiet running engine.
You could probably set up a dial indicator on one of the valve tappets and a degree wheel on the harmonic balance to determine if the cam is out of time, but at 155,000 miles it may be a needless effort. I think I can say with some confidence that it's too bad you didn't go on in when you had the water pump off. Oh well......
FYI - Here's a site for DYI Dakota owners:
http://www.dodgedakotas.com/cgi-bin/amb/view.pl?board=v6
It has a few fairly knowledgeable people, and somewhere on there is a very detailed article on replacing the timing chain. (Keep in mind, it's no "Brickboard" though.)
Good luck.
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