A couple of years ago when the MP first came out, there were reports that the MP's had a bad smell to them. It could get so intense that it stank up a whole room. People changed PSUs, logic boards and various other parts. Usually to no effect. Some even overreacted and grew scared of the smell.
My Mac Pro had the same problem but I didn't mind so much. But recently, I upgraded my CPUs and decided to finally have a thorough look for the parts causing the smell. To me, the odour was that of rubber. The kind of latex rubber used for bicycle tubes and, well, condoms.
Luckily I didn't have to search long: as it turns out, Apple uses two (actually three) strips of this rubber, about 1.5 inches wide and several inches long, on the sides of the CPU cooling towers to keep them apart and cushion them. Unfortunately, these towers get hot and that gives you that strong latex smell - especially when you stress the CPUs, which is what some people did to try and get rid of it! This smell is blown straight out of the machine by the dedicated CPU and exhaust fans.
So I took those strips off, replaced them with some other foam with comparable thickness and voila: smell is completely gone. The strips really stink, but that's latex rubber for ya.
Hope this helps anyone still living with a smelly Mac. Oh, and have some Apple tech change the strips for you if you don't like working inside computers. Taking the CPU coolers out of a Mac Pro is quite a task.
I'd worry you might affect the cooling capabilities of the CPU which in turn could cause the machine to unexpectedly shut down on its own if not pose a fire hazard. Are you sure the insulation density and heat distribution of your new material is the same? If not, keep an eye out to make sure nothing crazy starts to happen.