I recommend inputting your tool length offsets into the simulator. If you have Kinetic Control v5.5.3 or higher, there is a simulator tab directly on the control which should automatically simulate with the tool lengths currently set on your machine. The Joint 2 limit errors are about the Z axis not being able to reach a portion of your program, which is dependent on your work offsets and tool offsets. The simulator has default values set for them, and it may simulate fine with those defaults, but once you have real values in there that could change. The simulator will also make recommendations about pulling your tool out by a certain amount (or shortening it if necessary).
I used the simulator within the Kinetic workspace and found the problem. Thanks for the help. Part was cut out successfully! On to the next challenge! Thanks!