I had a the same problem on my F250 5.4L 2V, did the plugs, coils, both o2 senors, Throttle position sensor, Had the cats checked for flow, fuel, filter, and a couple other things too. What finally fixed the incredibly weak power (and occasional miss under hard acceleration) was ...a rebuilt set of fuel injectors that I bought on E-bay for about $100. Seeing as you've already done most of the things I did, it's a small price to pay to rule them out. Bonus for me was a 2 mpg increase right before a 4200 mile trip, they paid for themselves immediately.
2013 F150 Platinum 3.5L Ecoboost
2011 F150 Lariat Plus 3.5L Ecoboost (traded in on 2013
2000 F250 Superduty XLT 5.4L, 5 speed manual w/granny 1st gear
2001 Expedition XLT 5.4L (Ex wife got to keep it)
1990 Bronco XL 5.0L (gone but not forgotten)