sounds like coolant temp sensor perhaps, usually a cause of bogging and richness around 4k RPMs, esp if it only starts once u warm up. also if this is a newer car you just got, it might help to go ahead and do some routine maintenance on it like check the o2 sensor and TPS voltages, to make sure they are working within spec. the MAFs could be a factor too, swap it out with someones for a day to check that as well.

verify fuel pressure is set to stock.

the valve cover Tee isnt the PCV valve, that is on the rear passenger side that splits into 2 and routes into the intake runners by the injectors/head. but that is part of the system, and should technically be reconnected to the intake pipe, but i would have a catch can inline so it doesnt gunk up stuff.