To answer your original question...Go ahead and do whatever you wish to it. Auto or Manual. You can't hurt these engines. I don't see what the difference would be between auto or manual as far as modding the engine would be. Personally I have a cummings that kicks out close to 1000 ft/lb of tq and roughly 425hp, which is manual and is greatbut I still get my but kicked by a similar truck that is automatic. My bmw is auto and I beleive will do justice over a manual in a short burst.
Just my .02