Just rebuilt my UI and thought I would share some thoughts on matters discussed here.
Regarding the sniper training tracking - I am using Class Timer and you can easily add custom buff/debuff tracking in there, for example I added Sniper training, Lock and Load, Hyperspeed Acceleration (engi haste gloves), Reflection of Torment (Mirror of Truth proc buff) and Misdirection, its a great way to easily track your specific auras.
Event Horizon is simply an amazing addon, if you want to track any other spells that are currently not in there, just add it to the config.lua, follow the pattern and enter the spell ID of your desired spell. Easiest way to get one is go to wowhead, search for your spell and copy the ID from the url, it matches the game one, for example Concussive Shot (just as an example) is
www.wowhead.com/?spell=5116.
Regarding global CD and threat watching (among many other very usefull options) I can suggest IceHUD, which has these as very configurable modules, if you do not like huds, you can even play with the settings and enable just few modules and move them around and shape, so you have just a bar for what you want.
Misdirection - I found the easiest way to do this is simply use Clique (I am using that plenty for my healing chars, for hunter the MD is probably the only useful thing), choose a mouse button (or with modifier combination) and you can MD by just clicking the unit frame of the tank with what you selected (I'm using middle). You MD without ever loosing your target or any other fuss, I found this to be the most comfortable solution by far.