Hi Lewis, there isn't any setting for modifying the join tolerance, it scales automatically depending on the size of your objects. But at "regular object size" like you've got here the join tolerance will be 0.005 units - any edges within that distance of each other will get joined. If you scale your object down by 1/10 it will still be at "regular object size" but with a smaller gap between edges, that's effectively the same as increasing join tolerance.
So one process you can try to force edges to join with a looser tolerance is to scale your object down by 1/10 or 1/100 in size then rejoin it by using Edit > Separate on it followed by Edit > Join and then scale back up again. To scale something quickly by 1/10 select it and run Transform > Scale. At the first prompt to pick the scale origin type 0 and push enter to specify 0,0,0 as the scale origin, then at the next prompt where it asks for a scale factor type 0.1 and push enter. To scale back up after the rejoin repeat that but use 10.0 as the scale factor.
I just sent you an e-mail showing the location of what I think is causing the most problems, it's a spot with a tiny edge in it that is making an improperly formed trimming boundary for the surrounding faces. I sent you a file where I've rebuilt the faces around that spot and it should now behave properly for you I think.
- Michael
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