I suspect you are making this more complicated than it is. Many of the things you are concerned about could not be causing your problem.

If you have compression and you have a good spark (nice blue, not yellow), but you still have a miss, well, you have a fuel problem. Your problem is isolated to this cylinder and it could very well be that what caused the cylinder to be "dead" before the valve job was not the valve, but the fuel problem you have now.

The injectors don't often go bad, but has yours? Seems like you should be looking at the number 3 injector or perhaps the fuel distributor itself.

Good luck, and please keep us posted.

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2012 E350
2006 Callaway SC560