No they will usually come out as I say in the instructions, just be careful what you pry on.
I pulled out the injectors with a little prodding with a wooden spoon (don't tell my wife) and the crossover tubes I pulled them out with my fingers. You'll be amazed at really how simple the whole process is.
Here is what I discovered when I did mine for the first time last week:
Make sure your engine is clean prior to starting, it doesn't have to spotless but clean.
If your doing all 6, take your time and removed the intake manifold and heater grid as well as the engine lift bracket.
I laid out a towel to put all the removed parts for each cylinder so I could put the same cross over tubes, rocker arms, nuts and bolts all back in the same cylinder.
Don't try to fudge things by not using a torque wrench.
Pay attention to the details such as how things come apart and things like sealing washers and o-rings are all in place prior to reassembly.
Be careful laying across the radiator when your working on the rear cylinders so you don't damage the radiator/condensor.
Those are the things I thought were the important points to remember and thoroughly read the directions before you start.
Good luck