The inlet manifold wasn't removed,iv swapped the coil packs over still misfireDifferent fault codes, so you're starting again now. As always, internet diagnosis is always only that, one person who has never seen the car telling you what it could be.
Misfire is a problem with either fuel, air or compression. Since you've had the inlet manifold off, is it sealed back on properly, did you mess with the throttle body or IAT sensor?
The plugs were recently replaced? What happens if you swap the coil pack from 3 to 2 for example (edit:not sure if the cables are fixed to the coil packs, if so, difficult to test).
What condition are the injectors in? Does the fail follow the injector if you swap it from 3 to 2 for example. Last time I had a misfire it was a faulty injector.
When were the valve clearances last done? Has the timing been checked?
The list can go on really.
You've mentioned chain and compression test above, what has made you jump to those in your comments above. What's the mileage. What aren't you telling us.
spark plugs recently changed and service valve clearance done
the EML comes and goes stays for 1 day then goes off the next day