I have had similar things since the 4.1.2 update as well, and it was the same whether rooted, ROM'd, or stock (FXZ'd back to stock which is better than a mere factory reset).... anyways, it all mostly stemmed from the stock android browser. Most of the problems all were surrounding the stock browser, keyboard stutters/delays/words typing several seconds after they were actually typed, etc...webpages being stuck for excessive times... homescreen stalling or delaying mostly after browser use...you get the idea, not sure if this sounds all very sililar to your issues but what I have noticed is a huge improvement after installing and setting Dolphin browser as my default browser. I tried basically all the browsers and I noticed my Bionic improved dramatically once I stoipped using the stock browser.
Anyways, it's a suggestion.