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In an effort to continue down this rabbit hole here is where I sit.

I have continued with one of the original ideas before I attempt to try the build the autonomousCommand just before running it. To better discusse the code here is a link to the Github repo
https://github.com/GraniteCiyGearhea...ntsABot_Talahi
If we drill to

FIRSTStronghold2016/Copy of SirAntsABot_Talahi/src/org/usfirst/frc3244/SirAntsABot/commands/Auto_22_Demo_03_Drive_N_Score

We can see we are driving the Bot with a few commands before we:

addSequential(new Auto_Score_Ball_In_Goal());

This Code is now executing as I desired by only shooting if the goalChooser is not zero. Thanks to kylelanman for pointing it out we need to start the commands.

Now the trouble I'm having is getting the next sequence to continue when

Auto_Score_Ball_In_Goal()

is done. I have inserted some prints to show me who's end() and interrupted() methods are being called. The time out was just a test in Auto_Score_Ball_In_Goal(). I have also tried to use !c.isRunning. If you look at what c is its a command group called "PinBall_Cycle". This group sets the claw and shoots the ball. I also put system.out.println in these end methods to see if they are completing. It seems to me that everything works as planed and completing, only I'm not returning to the Auto_22_Demo_03_Drive_N_Score to finish the last two commands in the group.

Maybe someone can point me to or explain to me the life cycle of a command and what is needed to move onto the next sequence in a command group.