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I just had my stock 4-cylinder rebuilt completly, me and my dad put it in the other day and when we cranked it up it made this loud vibrating noinse that you can feel and hear from insided the truck better than on the outside of the truck. Its about where the motor connects into the transmission but im not sure. I thought it might be the pressure plate or the bearing. Anyone know what it might be.

There are a lot of things that it could be. Pressure plate bolts not tight, flywheel not tight, bad throwout bearing, bad/missing pilot bearing, bent tranny input shaft. Does it go away or change at all when the clutch is pushed in? Did you replace all the clutch parts when you put it back together?

It sounds like a clutch thing to me in general, but I can't rule out that the motor may not have been rebuilt correctly. Not much could cause a vibration like that though, not without being obvious and pretty catastrophic. Sure its running on all 4 cylinders?