Push pellets through the barrel with a rod to feel how tight they are in the bore. If the pellets go loose ahead of the breech, then that could indicate a constriction near the breech. That constriction could be left over lead from when the airgun was hard to load.
Ideally there should be some drag on the pellet all the way down the barrel. It sounds like by shortening the barrel, there is no choke, so it is important that the pellet not be sized down at the breech to rattle all the way down the barrel.
Other than left over lead, overtightening the barrel retention screws can spring the barrel out of round, This is a partial choke, and if there are two grub screws, the choked section can be wider, or wide enough to cause trouble. If the screws were tight enough to yield the soft steel, then the barrel could have "reverse dimples" at the screw locations. If you can't see such internal dings, you might be able to feel them when pushing pellets through the bore. Hopefully there are no such permanent dings in the barrel.
Try pushing pellets from the muzzle also. The crown is likely to make it harder initially than pushing from the breech, but the same idea of feeling how the drag varies down the bore applies.
Look at the rifling engagement on the head and skirt if pellets pushed all the way through, VS partway through and reversed back out. That will also tell you if your pellets and barrel are matched; and if there is a burr at the crown. Depending on your re-crowning method and how gentle you were, the new crown may have rolled the edge of the steel inwards. Troubleshoot as if you don't know anything about the barrel. Suspect everything.
If the pellets are not sloppy loose in the breech, but the pushed pellets indicate that the bore at the breech is tighter than near the muzzle, then biased lapping to even out pellet friction may help. Some people deliberately use more lapping stroked towards the breech end to create a subtle taper down towards the muzzle. Think of it as a long but very gentle choke that ensures the pellet is never free to yaw or rattle down the bore. This assumes the pellets are not to small for the bore. In that case, you need larger pellets, or a new barrel with a tighter bore.
If there are dings inside the bore opposite the grub screws, you may be able to lap those out with a "hard lap". One made from lead cast into the bore around a brass brush. Or a lead slug that has been "bumped" up in diameter to keep is snug.
Barrel retention screws should be nipped very lightly to avoid springing or dinging a thin soft airgun barrel. To prevent the screws from coming loose, use Loctite. I like wicking Loctite that can be applied after I am happy with the grub screws. Tightening those screws to the point where your concern is stripping the threads would definitely spring or ding the bore shut enough to matter with an unchoked barrel. With a choked barrel, you might get away with it.
