Hi, The 'knocking' you hear is the dual mass flywheel most likely responding to the miss.....it can sound like a diesel if the miss is bad enough. The noise from the d/m/flywheel also sounds like a very bad rattling.
I guess you checked the plugs for fouling?...or if they are too clean? I have heard about people having failure issues with aftermarket coils but the OEM stuff is usually reliable.
Just a shot in the dark....if yours is a 90-91-92 the OEM injectors fall pray to the ethanol in the gas today and in the early coil failure stage exhibit a ' slight miss' due to the gas shorting the coils...the ethanol eats the early epoxy insulation....the miss usually gets real bad real quickly though as once the insulation disolves things go south quickly.
You can ohm out a pair of wires + that coil by reading the ohms from one plug end to the other thru that coil assigned to that pair of wires...or you can just use a spare plug and pull a wire and give a look at the spark intensity, they show a strong arc when tested that way...no mistaking a good wire & coil it's a strong visable spark even in daylight.
On the injectors, if they are bad enough you can smell a lean condition thru the exhaust. Also, usually till the coils get real bad, upon start up from cold they work okay. It's not till the coils get hot that they start to short out & cause a miss....it almost seems that there is no miss at cold idle, but it is there but very slight & it gets worse as the coolant temp comes up.
This is another shot in the dark, the MAP hose is okay? No oil in it...that's bad for the MAP sensor....and it's connected, they blow off sometimes if the motor backfires....
sorry I'm not trying to be a wise guy, but that will cause a miss too.
Miss plus the weak starting (not hard starting like it's flooded) usually leads me to check the ingnition first but you have that covered.....unless ya closed a gap upon plug installation....(again not trying to be a wise guy).....but with the early Z's the injectors were never intended to work with ethanol, so they become a prime suspect. Oh yea almost forgot...vacuum leaks, large & a bunch of small ones will make for an ill running LT5. Check the entire PCV system for cracked rubber fittings...ya know over time & all.
Forgot this too....fuel pumps PSI, and the strainers (socks) and check the regulator hose for gas. With the plenum off you can see if the spray is okay or if some are weak/not spraying....and you can ohm the injectors but cold usually they ohm out okay unless they are really bad, but then that = a big miss.
Tom