Jim, This clatter is a bit of a strange one. Reading your first post I thought you had conventional shrouds, with or without headlamp ears. These are firmly tied to the lower yoke by the pinch bolts and there is usually enough slack in the mounting hole to lift them up against the top yoke before a final tighten. So there should be no movement here.
Then it turns out you have gaiters and exposed stanchions between the yokes. Some folks simply cut away the shroud above the mounting holes, but again the remains of the shroud are tightened against the lower yoke by the pinch bolt. Again there should be no movement or rattle.
A further possibility is the top of the spring is covered by a shroud similar to a plunger rear suspension spring cup or S/A damper spring cover. This should be clamped against bottom of the lower yoke by the spring exerting pressure between the fork slider and the yoke, a gap here, with the bike on the stand, means the springs are too short for the legs. Too short a spring means the ride height is lower and suspension movement from rest (off the stand) is also less, with a tendency to bottom. Reading the post mentions a spacer, but in use even a short spring will be under tension to carry the weight of the bike, so no shroud movement. but the suspension will bottom easily. Sounds like legs and springs don't match. Top fork bush movement is detailed in Roger's post on setting up his forks. Homespun spacers made from a crudely cut length of steel tube were what we used to restore ride height to tired, shortened springs.
My thoughts are to compare the spring length with published specs and the old springs, and also check the forks contain the correct amount of oil....too little and they will clang and bang as the the bottom of the leg hits the bottom of the slider, without the hydraulic cushion. I do not think the problem is the shroud itself, more a too short spring hitting the shroud after a large suspension rebound. A picture of the set up would help.
You would think simply changing the springs would not require new oilseal holders....If the spring diameter was wrong, what chance of other manufacturing errors?
Swarfy.