@desmond_ based on what I see in the chapters...
- I'm seeing a lot of odd edges. If you set your photoshop background to white, you can very easily see the edges where you didn't fully crop away the black. It'll also let you more easily see dark spots/yellowed paper at the edges where you can just white it out with a white brush tool
- I can see a lot of spots of paper texture in the margins between panels and the page edge. I have no idea what your raw quality is or how you're filtering/leveling the scans, but you can use a bubble cleaning action to clean the margins - just use the wand tool to select the white space and run this action https://mega.nz/#!yLZk2IYI!P21hbQUlrhcrPgip-Jr3_2zpUUP2hQHHnuPve3XmMDg - Note this will also erase the art if the art is not enclosed in a panel. In those cases, it may be better to brush out the dust by hand instead. (the page number will also be erased, that may affect whether you want to do this or not)
- Rotate before cropping, though you may actually just not be cropping to the page edge. I'd recommend cropping so that you don't see any of the page edges at all. Even though that means you'll crop away some of the edges of the pages since they're never printed straight, manga artists never put anything important near the edges of the paper because of imperfections in the printing process. Not that you should carelessly crop away, just don't feel bad about deleting the edges. For art that does matter, you can redraw in the missing edges or crop more carefully.
- look at the section about cloning errors here https://fascans.com/featured/basic-redrawing-tutorials-part-1-using-clone-stamp-tool-effectively/
- can't tell if you're using it, but usually people will put a black piece of construction paper or contact paper (any matte flat thin dark surface) between the paper and the lid to avoid art bleeding through to the other side (it affects areas with screentones), though I haven't seen any problems with that yet. (possibly top right page 18 on chapter 2?) It's essentially impossible to recover from it once you're past scanning.
- it's standard practice to resize every image to a consistent height. 4000px height is a pretty accepted value, but if the images having different heights doesn't bother you you can just keep doing what you're doing.
- I wouldn't bother backtracking and updating stuff. English typos and glaring mistakes aside, forging ahead is better for motivation and a better use of time.
Oh yeah, learn how to use typesetterer, presets, actions, and the bubble cleaning action sooner rather than later.
Also, I only ever wrote the dusting guide. Everything else was written by other people, so the only thing I did was link them
They deserve the credit for taking the time to write them.