The way I think of it is fuel=power=higher egts, air=cooling=lower egts. The injectors (or a box) are what add the majority of the power, where the turbo is what provides the "cooling" to keep the exhaust temps in check. The turbo itself doesn't add much power (maybe 20 hp-ish or so for the DZ), but the extra air that it puts in the engine allows more fuel to be added, which is where you get the additional power. The turbo does change the way the power delivery will feel (i. e. more bottom end or more top end), typically with the larger turbos and housings putting more on the top and less on the bottom, and smaller turbos vice-versa. I think that's why the hybrid turbos (like the DZ) have become popular for this engine as a really nice mid range solution.
As far as housings, the non-wastegated variety is significantly less costly that a wastegated version. There is a point in a turbo's output where if the pressures get to high, the heat required to generate any more pressure will cancel the cooling effects of the turbo and EGT's will start to rise again. With an HX35 (for example) that occurs at about 34ish psi, so this is where you'd set the wastegate to limit boost. Any more psi's are useless, or could even hurt the EGT cause.
The difference between 12cm, 14cm, 16cm, etc. is the cross section of the exhaust turbine housing (the part that the exhaust blows through. Smaller cross sections result in more velocity through the turbo, thus higher turbine wheel speeds and more boost for a given exhaust output for the engine. But, smaller cross sections also mean more restriction, so when the power levels increase the exhaust can't get out of the engine fast enough and egt's will rise. This is how you can "tune" your turbo to fit your fueling needs. With just the Mach 2's you probably wouldn't need any more than a 12, maybe a 14. Once you add a box I'd say at least a 14.
Boost and timing advance can kill a headgasket. I'm planning a DZ with a wastegeted 14cm housing to control the boost and swapping to a Diesel Dynamics box to reduce the timing (compared to the standard EZ and Comp).
As far as clutches, you'll need one. The stocker might last a while with just the injectors, but add a box and it will be history. Also keep in mind that you'll be getting into a hp range where a improved fuel system will be needed for a healthy injector pump. And finally, the exhaust will work with the DZ turbo, since the back half that bolts to the exhaust is still an HX35, which is what you have on your stock truck.
Geeze, I didn't realize how much I've typed. Sorry to be so long winded.