Just went through the same issues chasing some heavy shaking at idle.

Replaced the injectors, adjusted the valve clearance, retimed the IP, checked for chain stretch, purged with cleaner, replaced the fuel filters, blew out the fuel line to unclog the strainer, checked the compression (325psi+/-5psi), nothing worked. Drove me nuts.

Then I replaced the injection pump. Voila. Smooth as silk now.