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I don't have a boot on mine, and the Cat is right below it, and it is a short shifter, so I know it's going to be hotter than most, but I'm wondering if I should do something about it right away. Would you do me a favor, and see if your shft is really hot after a good drive?
Mine's like IM with ThermoSpacers after a hard drive hot. I can hold it for about 30 seconds befiore it gets uncomfortable.

Mine isn't, but when my friend has his shifter fall through the floor and it was resting on the exhaust I remember it got pretty freakin hot

Change your gear oil, helped for me.

Is the heat deflector plate still installed (probably not eh?). Burn Baby burn.

Are you usng the stock shift knob or an aftermarket metal one? The stock one would prolly be cooler than the metal one (if that's what you're using)

I have a the OEM knob, and it doesn't get too hot, but today I drove for about an hour with my car loaded with stuff, and I couldn't touch the shaft for more than a second. It doesn't have the heat sield.
I wil change the gear oil, and wrap the exhaust again..

I would recommend Amsoil MTG or a MTG/MTL mix, that's what I plan to swap to once I change mine out. People have said synchromesh works great as far as feel, but from some UOA's done it doesnt look like it holds up in the wear department quite as well since it's too lightweight. Since its cheap, you could always be the guinea pig and find out!