How far should the alignment tool go in, mine goes in about 1 in with markings on bottom but not top, I don't know how far it should go in, being my first time, should it go to the first stop on tool? which is about 3in.
Yes, it should go in to the drive coupler to either the shoulder on the tool (3 inches) or bottom out in the coupler. If not, that means that the drive coupler is not lined up with the gimbal bearing.