The 3000rpm rumble isn't coming from your gear box. It seems to be a very common problem with Altezzas. There's been lots of talk about where it actually comes from, but as of yet I dont think anyone has pin pointed it as such for an easy fix. Have a read of this thread http://z4.invisionfree.com/lexusaltezzaclub/index.php?showtopic=962
As for gearbox oil (I assume you have manual?) you must use a GL4
or lower spec oil in your 6MT anything higher i.e. GL5 (which a lot of synthetic gear oil is) will causes the brass syncros to wear.
I'd recommend Redline MT90
or TRD 75W90
. Redline is GL4 & TRD GL3 which is what Toyota recommends. Both are fully synthetic too. There will be mineral options (like VMX) but Im all about the full synthetic oils in gear boxes & diffs due to the long service intervals & abuse they take.
Also dont put any additives/friction modifiers in your gear box oil, they will affect the GL rating.
If you have an Auto Trans get some genuine ATF from your local Toyota dealer.