just going to say, walls of text

Runes are completely suboptimal in all scenarios because Marks and Quintessence should be AD (or maybe ArPen), Seals should be Armor (waiting for the upcoming changes to Runes) and Glyphs should be flat or scaling Magic Resist.
Your choice of jungle item is good, that's it. Consider items like Randuin's Omen, Sunfire Aegis, Banshee's Veil and Black Cleaver instead of Atma's Impaler, Bloodthirster and Ravenous Hydra. Trinity Force is an option but in most of your games an early The Brutalizer is your only offense choice next to your jungle item in the early stages of the game.
Think about adding coding to your guide because this way it doesn't look suitable.