Step 1: How to scan larger-than-letter/A4 sized pages from a book?

For scanning, don't need to perfectly align to a page size using the scanner. Use the scanbed, put the page in the middle - we'll crop later. Scan all the pages using this method. Scan to JPG files.

Step 2: How to crop them efficiently?

In GIMP, drag the first page in, manually select the desired page region, then right click -> image -> crop to selection. This will crop the canvas to the desired page size.

Drap the 2nd page in. Note that it's on the 2nd layer. Notice that only a "window" (of selection size) of the 2nd image is shown. Use the drag tool to move the desired portion of this image into the "window".

Repeat the above process for the rest of the pages. Now you should have each page in their own layers.

Rotate Layers

Shift-R (or "Tools -> Rotate") for layer rotation (not whole image). Drag to rotate. Shift-Drag to rotate at certain degrees.

Step 3: How to compile them into PDF?

GIMP 2.10 supports exporting layers as pages to a single PDF file. Export -> set file name to some_thing.pdf -> press export. A dialog pops up about PDF exporting, choose "layers as pages" (it lets you specify the order).