Disconnect your gamepad or change this variable in SkyrimPrefs.ini to:
[MAIN]
bGamepadEnable=0
because this is the main reason you don't have almost any control over the game with your keyboard and mouse (until you open console or tweak Data\Interface\Controls\PC\controlmap.txt).
If it doesn't help, you may want to temporary disable antivirus software (it may block Skyrim to recognize your input) or do a complete reinstall again, but this time play the game without any mods. If you would have no problems, install ENBSeries, try playing the game again, then SKSE, play again, then one mod, play again, and continue to do like that one by one until you have same problems.
FYI, this article may help you.
http://www.nexusmods.com/skyrim/mods/56894/?