Annoying vibration and grinding.

What tranny are you using? You have serious transmission problems. If you keep driving it, it's gonna ground you soon. Got AAA? It sounds like your case itself may even be compromised, but at the least you have major internal problems. Whichever T you have, you have too much engine in front of it.

OK, clarrify some of this for me

When ever im in 1st or 2nd gear and I push the clutch in it grinds...everytime I put it in 5th gear It grinds the whole time

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So are you saying that actually pushing in the clutch while in 1st or 2nd makes a grinding noise, or shifting into one of those gear it grinds while shifting? Or is it like what it sounds like your saying about 5th- it constantly grinds while in gear? Does it do it regardless of how fast you are going in 5th, or is it a highway speed only issue? I think there are several things wrong, and all of them are in the tranny. However, driving while these symptoms are happening WILL cause damage to other components, if they haven't already. Don't keep driving it! Thankfully, T5's are cheap and at the very least you should be able to find another one for a couple hundred bucks to buy you some time; and it's relatively easy to swap it in. Good luck

Major internal damage.