Figure out if it is air, fuel, or spark before you worry about anything.
Do you have any reason to believe any of the cylinders aren't getting air? This usually isn't the problem when there is a miss.
A flow test on the injectors will tell you a lot. Pull the bank of injectors and see how the injectors are spraying and if all in relatively the same flow rates.
I like to simply:
1) put my timing light on the spark plug wire and test for a strobe while cranking.
2) pull the spark plug out and put it in its plug wire boot and ground the plug with a jumper cable on the threads. Then you can observe the strength of the spark.
I bought a 1973 450sl that was vandalized and when I first got it, it would run, but VERY VERY poorly. I tested for spark as mentioned above finding that 6 of the 8 plugs weren't firing. I put in 6 used plugs to fix the problem.
Before = running on 2 cylinders:
(I've since cleaned the car up much more.)
Once you figure out what it is, you can usually see how simple it was to fix. ... And I was fully intending to part the car out as soon as I heard that. 6 used spark plugs. That's all.