Frame stiffeners, extra weather stripping on the rear hatch, extra undercoat underneath.
I also totally took my dash apart, and replaced all the felt with new thicker black felt. It sits between all the plastic contact points, and really quieted it down.
We got a sunny day up here on Wednesday, so I decided to go ahead and spray some more of that duplicolor under coat. Works pretty good. I don't know if it makes a huge difference in sound, but it stops rust well.
do you have a bored out throttle body now? or a stock one. The 63MM is pretty bling but if you want to save some $$ is a pretty easy DIY to take the taper of the stock one and have a 60 MM straight through.
after i did all the head work on my 2000 (swaped 7120 head) along with the header, cat and muffler i noticed a little bit by taking the stock taper out my TB, whether there was any actual gain i dont know. The way i see it, the throttle body isn't the biggest restrictor in the system. With the 63 MM TB would the intake manifold need to be opened up to that dimension as well? Do you have any other stuff done the intake side of the motor?
Did you ever fix your vibration? If not I think I would definitely look into your transfer case. Mine just took a dump on me and I'm noticing that as it worsens, so do my vibes. Just thought I would throw it out there