There are extra spacers provided to help with this situation. This stems from the fact that there's a lot of tolerances all stacking together - how long the auger is cut, how far the barrel goes into the auger before it bottoms out, how long the barrel is, etc.

In your situation I would recommend setting the shaft collar at 90mm, and using one set of spacers between the motor and the chassis.

The main bolts are the correct length, the ones in the photos were during the prototyping phase when I was still working out how much length was needed. By the way even if the bolts were longer you couldn't just put more spacers on, as that would shift the whole enclosure over 6.5mm.

When I get to step #9 I have ~11.5mm of feed screw sticking out of the barrel; the instructions say it ought to be closer to 5mm. And at step #12 after I've attached the motor and hex socket I find that their presence impedes the thrust bearing from being compressed. I could solve these issues with additional spacers and changing where the collar attaches, but as seen in my third photo the provided bolts are just too short.

Collar is 84.5mm from the end of the feed screw, as per instructions.

~11.6mm of feed screw sticking out of the barrel. And the thrust bearing is as compressed as it can be in this photo (not at all). If the motor were removed so the bearing could be compressed it'd be about 11.5mm sticking out.

Close up of how I have things put together. I think adding a third spacer all around and changing the position of the collar would solve everything but as you can see the provided bolts just aren't long enough. I noticed a photo in the instruction manual showing bolts whose threads stick out about a 1/2". Did I get the correct size?

Please help and I apologize in advance if this is just me being an idiot,
Garrett