Got the hypertech PPIII, huge dissapointed?! Am I doing it wrong????

[96_4.6]

Just got the hypertech power programmerIII for my 96 mustang gt and even tested on a 98 gt they came up with some pretty decent numbers but i plugged it in and all i can do is change the therostat to 176, raise the rev limiter by +100 which i am unsure of what to raise it too and make my shifting firmer, for $370??? Lucky i only payed 200 off a friend i was hopin i could tune it for my high flow air filter and cat back cause i thought i saw something on the back of the box about it insted i get 3 options?? Where does the hp come from??? Thanks maybe i'm just dumb