You don't have any broken shift forks. If you did you wouldn't be able to shift at all. Been there, done that. The vibrating of your shifter is most likely due to the 4.10s. They will cause a bit of driveline vibration. That's why they come with the 10 pound weight from the factory over the pinion to balance the gearing and stop vibrations. The weight becomes useless after a gear change and can also be removed for a weight reduction.
The grinding is your synchronizers. They grind when cold because the tranny fluid has drained off of them. Just take it easy untill it warms up. BUT, with only 6K miles on it, unless you've been really hard on the tranny while shifting, it should not be grinding when shifting. The synchros in the T45 aren't known to be that great but they shouldn't be grinding yet unless you've been really hard on it. Take it back and have the dealer fix it. The gears should not void the warranty.
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