Looking at a 93 4Runner 3.0 liter. The engine starts and makes some clicking noises. After a minute, it goes away and comes back intermittently.
it's not loud. The mechanic at the shop says new engine. Every thing else is tight.
Im not convinced it needs a full replacement. I have read several posts here.

 

This is a job for your stethoscope, it will give you a location for the origin of the noise if it is mechanical.