bjowett,
There's a couple basic problems with an intercooler on the TRD SC. First if its not a total custom job, they're expensive, especially the air/water ones.
Second, on the air/air ones (which are generally the most efficient ones cooling wise), you'll normally see a 1-2psi pressure drop between the blower and the intake(even on the most efficient ones). On the TRD SC which is a 4-5psi system, you can already see the problem....you've just turned your 4-5psi system into a 2-3psi system trying to get the temps down to ambient. You can compensate for this by using a smaller nose pulley and spinning the blower faster, but the Eaton units really start to crank out the heat the faster they are spun. In addition, the faster you spin an Eaton the most parasitic hp losses you'll incur. There's definitely a happy point in there somewhere between blower speed and intake temps you have to find. For a turbo application, its generally much easier to increase the boost pressure without loosing to much efficiency to compensate for the air/air IC.
The air/water IC's typically have a much smaller pressure drop (because of the inherent design). They tend to work better with low boost SC applications. The better ones are quite pricey though. A friend of mine custom did a spearco a/w IC for an Eaton unit and it still cost him close to $1,000. I've seen at least 1 custom a/w IC on a cruiser though.....I think it was post on the 80's cool list.
Mike