In the pictures below it can be seen that the E1 extruder mount sits lower than the first.
The following picture highlights where it is interfering
We attempted to change the position that E1 rests as suggested by @west, by loosening the fastener securing the actuator to the actuator mount, pushing the actuator up, and tightening the fastener back down. This did not alleviate the issue.
I had not previously seen the extruder down that far. @MikeR said another unit he had was opposite; E2 resting farther down than E1.
I also noticed that the old rev actuator connector was used with button head fasteners, as a result the button head fasteners are about half way seated inside of the pocket meant for socket head fasteners. I couldn't see an play between the actuator and the actuator connector as a result of this however.
This was on QB12, we tried another fan shroud without any luck.
I asked @paulette to reassemble the tool head and continue trying to calibrate the machine, noting down any issues she has along the way that may be related such as interference with wiper mounts or the Y cable cover.