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Heres what I would do if that was my car.
maintenance related:
#1 boost leak check (just to be sure)
#2 plugs look GREAT so leave those put.
#3 degrease/clean the compressor inlet rubber piece
diagnosis related:
#1 Check grounds, especially coil pack ground at the back of the head. Inspect all coilpacks and clean them up a bit.
#2 swap maf for a known good maf. You have a redtop? So use a KA24E maf sensor from a random 240 in a junk yard.
#3 change the knock sensor / verify the wiring is intact
#4 block off the bypass valve (blow-off) so that it can not release air and run the car.
#5 change the Coolant temp sensor
#6 change the fuel pump and fuel filter and fuel sock. verify fuel pressure
Bogging issue... its either a weak spark, too much fuel, too little fuel or leaking compression (leaky bypass) intermittently. the reason I lean towards spark is because your plugs look good and your cold performance is good, and you said it runs better at 5,000rpm which is why torque (and thus VE) is dropping. So not a plug issue, probably a coil ground issue or coil pack related.
But again, could be maf related / fuel related. Fuel sock / Filter I doubt since it runs good when cold. Once it warms up, maybe the fuel pump is giving up. So grounds first, then fuel pump. And the maf is easy and fast and cheap to verify (KA24E from junk yard) very simple might as well.
And last, knock sensor. Do not underestimate this guy. If the knock sensor is bad or missing wiring it will bog exactly like you describe.
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