Judges wont count it against you for faking the collars, but it definitely won't help your score like doing real layers would. (The kimono collars, not the odd number of haneri)
For the stitches, though tedious, I imagine a blind slipstitch or catch stitch would be the way to go.
Luckily Kubo doesnt really have a set era, the costume designer pulled from 300bc to present day. This gives you some leeway as to what fabrics to use. From what I read they tried to go with upholstery weight fabrics, though this was in part due to their stiffness and ease of filming (didnt move much between frames)
You may want to use a mix of upholstery, jacquard, and damask fabrics to get the right textures, weight, and patterns down.
This ones a little to dull, but maybe get a sample and see if you can dye it bright yellow for the outter layer
Along with some dye/paint to get the details such as the pattern on the sleeve and obi
The hardest one to do is going to be the lavender, as its stitched into folds to make a design. Here's some patterns
If you look up tutorials for fabric manipulation or smocking on pinterest there are a bunch of variations.
One way to lighten the under layers without faking the collars would be to make the collars and sleeve hems out of upholstery fabric or another mid weight fabric but attach them to a cotton shell.