Can the inlines be changed?
You mean the built in motor switch?, if yes, no it cannot be changed.

That or I set the clamp at the blower housing too far back. I set it all the way back to the motor
That should be good....loose and it may travel forward and hit the housing.

are they numbered from 1 -6 from top to bottom or bottom to top consecutively, or are 1 and 2 turned around?
If I have read this correctly, no the numbers don't normally go in order. Heat switch wires ( often #1 and 2 ) can be revered as they are just an open or closed switch for the heat and don't do anything for the motor running.

jeff.