I'm by no means a pro, there's def others far more experienced driving than me on here, but my two penn'orth worth...
Your trace length controls the pony position in the shafts in motion, if your tugs slide too far forwards on the shaft when in motion your traces are too long or shafts too short. Your breaching and tug stops are to stop the cart rolling into the ponies hocks as you stop, so shortening the breeching is moving your cart further back from the pony. You mentioned having shortened the shafts, in my mind that will have brought your tug stops further back and effectively made your traces longer. The cart balance is important too.
So long as your tugs cannot come off the front of the shaft and they seat back to the stops before the breeching engages fully then I wouldn't be too worried about them settling somewhere in between during motion. Do you have a side on picture so we can really see how it sits?
This is my guy Hank, we were just harnessing up here, at rest the tugs are on the stops, but would move forward a sniff when we got underway.
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