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4EAT problem? Help?

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So my dad and I just put my engine back in, replaced the head gaskets again and got the heads checked and machined. Got it all together just fine, and when I drove it there is a weird grinding sound coming from the back of the engine which we figured the tranny or maybe the starter was sticking a bit. Topped off the tranny coolant and oil, rotated the flex plate in trany(we removed when we pulled off the engine), pulled the starter and was fine but the sound remains. It gets louder as the revs go up, and randomly when you start the car. Hopefully this makes sense and wanted to see if anyone has ran into a problem like this, thanks guys :)