Just an educated guess but the LENGTH of the pilot bushings may be different? You can smear some grease on the front of the teeth of the tranny input shaft and stick it back in as far as it will go. Then remove it and check for contact marks on the face of the pilot bushing. If it is not too long there won't be any grease marks on it and the problem is elsewhere. If there are; then remove it and shorten it by the required amount plus a bit more for a hot clearance and reinstall it. Or get a new one and do the same procedure before installing it.
Not fun I know but what can you do?
