hello im trying to get some help figuring out whats going on with my mustang i bought it for 4500 with 86xxx on the odometer drove it home 2 hours away no issue besides general maintenance I.E(oil change, spark plugs, coil packs, MAF, oil pan gasket, valve covers (due to coilpack mounting brackets broke off or cracked), upstream O2 sensors and fuel filter other than that the code it was throwing was lean bank 1 and 2 upstream it has a low uneven idle ( cold start idles at 1000 rpm once warm lowers to 800 then fluctuates between the two rpm ranges) no rough idle or excessive engine shaking. got home and began work on it once i finished the tune up i began driving it more as i did i noticed its hesitant on its power 1st, 2nd, and third if i try asking for power it will come in and go out and by 3000 rpm in 3rd its got nothing power dies out. i also had changed the valve covers ( sourced from a 2010 ford f150 5.4) drove the car for a while after tune up not including valve covers and i noticed a tapping sound coming from the engine but at higher rpms it goes away. well i did research for a while can came to two answers but i dont know which one to go with

1. intake manifold flaps the actuator for them are going out ( ive never heard of this but i put my ear to the intake and i heard the tapping sound coming strongly from the intake) or
2. cam phasers are going out or bad (this one came up alot but the noise is not heard as strongly when listening from valve cover area using an extension as stethoscope).

so in conclusion how could i confirm one or the other no codes are present relating to either the cam phasers or the intake having any issues and the valve covers that i sourced came from a 2010 ford f150 with the 5.4 in it ( would i be able to use the 5.4 valve covers on the 4.6 the 5.4S has less bolts than the 4.6 but is the correct shape size and the bolts line up with the existing bolt holes for the 4.6) would it be ok to run them

sorry for the book lots of ripping hair out and lates nights im just trying to get some answers