Compared to the 84, the 87 won't feel like a Diesel.

I don't understand how it can be smooth yet not running on all cylinders.

Change all the filters and check that the fuel flowing into the IP is the color and consistency of commerically available Diesel fuel. Someone might have gotten creative with fuels.

Loosen each injector line one at a time while idling to see if one cylinder isn't pulling its weight. If you find such a cylinder, swap injectors to see if the problem is with the IP/cylinder or injector. Best to use new injector seals when you remove and replace injectors.

Does the 87 still have the trap? If not, remove the plug on the #1 exhaust runner and see if that improves throttle response. If so, the oxidation catalyst beside the transmission is likely clogged.

Sixto
93 300SD