I'm working on a 95 Aerostar(built 10/95, why not 96?) that loaded up with cookie crumbs and spun the number 1 connecting rod bearing. I purchased a crank kit from a local jobber and installed it in the engine. The crank was a different casting number and the counter weights were different, probably my first mistake installing it. Upon start up, it sounded just like it did with the bad rod. Great oil pressure but a knocking type noise coming from up high in the right rear cylinder. Tore the engine down and though I saw some marking from where the rear counterweight may have been touching the bottom of that pistion, everything else checked out fine, pulled down all the connecting rod and mains and checked bearing surfaces, torques, and everything looked great. I ground some of the counterweights corners thinking that if it was touching, it was just touching as no damage was present anywere. Startup and same knock. Tore it down again and this time popped pistions, everything checks out perfect, no broken ring lands and the wrist pins are as new. I let it run for at least 1/2 hour before tearing it down and nothing changed. Now I'm wondering, is it possible that the timing was changed on that replacement crank and this thing is firing that rear cylinder at the wrong time and this is the noise, maybe firing it with the exhaust valve opening? Wish I would have pulled that plug wire when it was running. After listing to that noise for so long, I could be convinced on anything, I'm grabbing at straws.The original crank is heading out for regrinding and I'll change it out again. I'm about at the end of my rope with this thing. Any help or ideas would be greatly appeciated. Thanks and Happy Holidays!!!

 

Is it possible you mis-routed one or more of the plug wires? Also, on some engines there were issues with the keyways on the front of the crank apparently making it difficult to line up the front pulley/timing wheel. Here is an article on rebuilding issues related to 4.0 engines from the Ranger Station that may be of interest to you.
https://www.ford-trucks.com/40rebuild.htm