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Optimum workflow for creating an audio-visual from scanned slides?

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I'd like some suggestions as to the best workflow to adopt when generating an AV from scanned slides. I'm transferring my 3-screen audio-visuals from slide format to Blu-ray. The slides are being scanned on a Nikon Coolscan, and after editing end up

I'd like some suggestions as to the best workflow to adopt when generating an AV from scanned slides. I'm transferring my 3-screen audio-visuals from slide format to Blu-ray. The slides are being scanned on a Nikon Coolscan, and after editing end up as ~100 MB, 5400 x 3700, Tiff files with seven layers. These files are then archived, separate from anything I do with them in Premiere. They'll be imported into Premiere, along with the original soundtrack, and eventually output to Blu-ray disk. Then I hire the local cinema for an evening or two, let the word spread, and we reminisce and party!
I realise that pre-conditioning the images – flattening, cropping, down-sampling to a suitable size – would be a good approach, but I'd rather avoid that if possible for two reasons: (1) so that I only have one image to keep track of, instead of the original and a Premiere version; and (2) if I decide to edit colour or contrast I can do so non-destructively on the original. The latter is an important consideration. Images may be used in more than one project. If I decide to alter the look of an image (not because of the look of the image within a particular project, but because I decide the original edit was inherently flawed), it would be better to alter the original and have that change reflected in all other uses of the image, than to alter, say, two copies of the image plus the original.
A finished AV will range from 30-400 images. The longer shows will be broken into sequences of no longer than about 20-30 images. These are some of my concerns:
Cropping
The scanned images include a small amount of the slide mount. That way I know I've scanned the entire slide. So that has to go. And given that slides are 3:2 and Blu-ray is 16:9, something else has to go as well. I've been through most of the Premiere PDF but have yet to come across a cropping tool. I know how to position, scale, rotate, but how do I crop? Scaling is not a substitute because I may want certain images to not fill the screen and not show the slide mount.
Flattening
Will layered Tiff files cause difficulties in Premiere or Encore?
Resolution
Will 5400 x 3700 files (versus resampling to 1920 x 1080) have a serious impact on the time in takes for any part of the process from importing into Premiere to encoding in Encore?
Image Order
Is it better to order and renumber images using Adobe Bridge, or should I just shuffle images around in Premiere? Working with Premiere alone would have the advantage that I can import the originals (if that is an acceptable workflow).
Packaging
When a project is finished, I want to package all the assets via Project Manager and archive them. And I'd rather not archive 100MB image files. Now, this is going to be a big ask, and I'll have to jump across to InDesign to explain. When I've used scanned images in InDesign, I link to the original 100 MB files. No problems whatsoever. Come archiving time, I package in one of two ways: use an InDesign script to crop and resample the original images, and then package; or I simply export to PDF, and during the export all images are automatically cropped, resampled, and saved within the PDF in whatever format I choose. A simple and elegant archive.
Does Premiere have the ability to crop and resample the stills it uses, and either overwrite the original or save as a new file?
That question has just made me think: if I do need to crop, flatten and resample before importing into Premiere, or for archiving, maybe I should be mocking up my Premiere projects in InDesign set to a page size of 1920 x 1080. I could drag in all the images, then shuffle, crop and size them. When I'm happy with the sequence, I export as jpegs, and get the cropped, resampled images that way, ready for Premiere.
Any comments most appreciated.

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Your last paragraph makes the most sense. Although a script in Photoshop would easily do what you want.
Before you resize them, make sure you don't really need to pan across them. Resizing down to around 4K or so might avoid problems.

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