there should b a rubber seal underneath the shift boot, if you dont have one it helps reduce the smell, and the noise alot, you can get them off ebay america
the heat coming through the trans tunnel i havn't really noticed, however it is hot to touch, i guess you could put on any type of heat sheild but if ur trying to make ur car light i assume u have to choose!
the smell is generally thought to be coming through the rear lights and hatch seals, there's a long thread on it at hyridz. i've been considering buying
http://www.airtab.com/ and putting them at the top of the hatch, either just before it or on the top of the windows so they are easy to pull off, and hope that it disrupts the air up there and makes it flow off the back of the car better, although might just hope they are doing that as part of their wind tunnel testing and see the results first, however it's not like they are that expensive. ppl on hybridz have been suggesting it as in this video
http://www.youtube.com/watch?v=KmVdufi3Bmo you can see the "air" seperating from the body starting up there, so if this delays it then it should dely the turbulance. the other option is the rear spoiler which i'm planning to get at some stage, and in which case i guess the airtabs would put more air over the spoiler like what they are used for on the evo's