A way to control the Render Heirarchy?

Hi,
I'm working with H.264, 1920x1080, 30fps video. Our final piece is going to be NTSC 720X486 (4:3).
When I cut the source material into the timeline, it is scaled down, the aspect ratio is adjusted and the frame is shifted vertically by 1 pixel. Once edited in, I fill the 4:3 pixel aspect ratio by scaling it up enough to fill the screen top to bottom and sliding the image left and right to get the composition I like, letting the sides get chopped off.
This larger frame size is very useful in that we can return the material to it's 100% scaled size and have some flexibility to re-frame and re-use some of the footage.
OK, here's my issue. I'm using a couple of filters to affect a film look, one of which is generating grain.
My problem is that the footage appears to be scaled AFTER the filter applies the grain, resulting in obvious changes in size of the grain pattern.
I tried scaling up a clip, nesting it and then applying the filters, which didn't appear to work. I tried a similar method of editing the clips from one sequence to another (nesting) and adding the filters; no go. I tried applying a filter that contained a scaling parameter, figuring that if it scaled the image back up the 100% without any degradation, it would allow me to dictate the render order. I didn't think would be a good method of scaling the image up, and it wasn't. The image is resized but it all happened within the limits of it's raster.
So I'm left with two methods that I think will work, one relatively certain and one marginally plausible. Hopefully someone else has some prior experience with this dilemma and will come through with some thoughts on the matter.
*Top Ideas, so far.*
The first thought was to adjust the grain size within the filter to match whatever percentage adjustment is made to scaling of the clip.
The second and more straight forward approach is to edit the piece and to export it out, then bring it back in and apply the filters to the whole thing. It might make sense to dice it up and deal with individual scenes that need separate attention.
So, does anyone have any insight or ideas on how to handle this dilemma?
Hopefully this makes sense, I'm very tired.
Thanks in Advance for your help.

No way to change the hierarchy, I'm afraid.
Sorry if you did this - but since I didn't see it mentioned exactly in this way - how about dropping your 1920x1080 clips into a 1920x1080 sequence, applying the grain filter, then nesting that into your master SD sequence so you can pan-scan?
You mentioned dropping your HD clip into the SD timeline, then nesting, which definitely won't work since FCP obeys sequences (SD) over clip (HD) when conforming mixed footage and how filters are engaged.
But if all your clips are 1920x1080 (as opposed to just a select few), then yeah, your best bet is to export, then reimport, to apply filters as needed. I suspect that what you're best off doing...

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