If you plan on going with twin turbos at some point, then the headers would be a waste, since you would have to get rid of it to install your turbos. From a horsepower stand point, shorties will give you nothing, and long tubes might give you 25 hp? A CAI and a canned tune might give you 15 hp? But if you are looking at installing a turbo system, you will have to trash the CAI, and load a new tune as well. So if you are planning on installing turbos, leave the engine alone, because pretty much anything you put on, you will have to remove when you put the turbo system on. If you do anything to the engine, then you may want to consider rebuliding it with forged internals if you plan on going over 500 hp. If you don't plan on going much over 500 hp. then leave it alone.
Turbos and centrifigal superchargers are typically set up to get peak hp at high rpms, where as roots and twin screw superchargers will give you more hp at the low end and mid range.
In regards to setting an engine up to run in a desired rpm range, the only thing that will really do this is the right cam for the desirted range. Turbo cams are typically a lot different than supercharged cams, which are different than high performance naturally aspirated cams. So I wouldn't swap cams untill you get you turbo system, and then get the right cam for the set up.
Don't worry about the low end and mid range if you are planning on going turbo or supercharged. You will make make more low end torque than you ever use. In fact, they biggest problem you will run into is trying to put 500 hp to the ground.
In regards to supercharging on top of turbocharging, (typically know as compounding) I would say just stick with a traditional turbo system or a traditional supercharger system. You will get more than enough hp out of either one alone. There is a company call Hellion that sells compounding kits for 03/04 Cobras and GT500's. I do not believe they have a setup for componding a 3V. Typically, they turn the boost on the supercharger down way low on these systems, and in the end, don't really make much more power than either a well setup standalone turbo system, or a well setup standalone supercharger system. They are also really complex, expensive, and definetly not smog freindly, so check the smog laws where you live first.
With a stock 3v engine, there are multitudes of turbo kits and supercharger kits that put out 430 - 520 hp without doing anything else to the engine. This might be a good place to start.