you also will want a radiator from a v8 dakota as well, the on for the 6 might not be up to the task especially if you want to tow, or drive hard, also check your rear diff, the 9.25 dodge is a decent rear for moderate power but some of the 6's ha...
the mod motors( 4.6 and 5.4) both use a coil for each plug put a spark tester (like a test light but made for checking spark in your 3, and 7 and see if your losing spark. also when you changed your plugs was there a bunch of crud down in the hole...
the 318 has always been a good runner, nothing over the top just a strong basic engine. with the upgrades it should be a bit of a handful in your dakota.
That sounds like the balancer, if it stops when idling and in neutral going down the road, and vibrates when in park and reved. U-joints and tail shafts/housings only affect when moving. check the harmonic balancer on the engine and be sure it is ...