IF your timing is off, it will definantly cause an erratic idle, poor performance, and the motor could barely run depending on how far it is off. If you put the distributor say .. a few teeth off (hypothetical) the motor might not even start.
As far as the loud tapping sound, I doubt you tightened the valve cover bolts too much, did you make sure to check your oil after you put everything back together? Put some oil in it, run it.. see if the noise goes away. If not get a screwdriver or stethoscope and listen for where the noise exactly is (screwdriver is backyard mechanic style, stick it to your ear and the other part where you want to listen).
To check if your mising a cylinder you pull a spark plug wire out, 1 by 1, while the car is running, if you pull it out and the idle pitch changes or performance changes .. plug it back in, that one is firing. Check all of them this way, and if you pull one wire out and it doesn't change the pitch...you know where your problem lies. You can also does this with the injectors in the same fashion.
Let us know if anything changes.
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