Does the new shifter have threaded bolt stops, if so you might have them to tight, back off the shifter stops a little. Also i made a gasket for the shifter base on one of my t5 trans cars that quiets down the noise a lot. So instead of using silicone on the shifter base, buy gasket material from the auto parts store and lay it on top of the trans shifter opening and cut out the gasket with a x-acto knife and bolt the shifter back on.