Will take a few drive cycles for misfire code to return.
Missing is caused by 3 things
The noise you hear could be from a broken spark plug arcing.
New just means never tested now a days, so never assume a new part is good until it is proven good.
Or the noise could be from mis-wiring of spark plug wires.
The 5 6 4 side always gets me, check it twice and then a 3rd time, and make sure #5 goes to #5 cylinder, same for all the other, #1 and #2 as well
To test for fuel issue, unhook the coil, the 4 wire plug
Crank engine a few times
Remove spark plugs, each should have a wet tip if it's fuel injector is working.
Compression, well compression test is the only way.
4.0l SOHC had issues with timing chains, it would often start off as lower power and a misfire, compression test will show if both banks have equal compression, if one back is low then chain on that side has slack or slipped.