I have 2 pdf files scan0126.pdf and scan0125r2.pdf and I need to combine them however page scan0126.pdf contains page 1 and 3 of the combined document and scan0125r2.pdf contains page 2.

Re-order selected pages from multiple PDF documents into a new combined PDF

pdftk A=scan0126.pdf B=scan0125r2.pdf cat A1 B1 A2 output combined.pdf

# you can also use ranges
pdftk A=scan0126.pdf B=scan0125r2.pdf cat B1 A1-3 A16 output combined.pdf
# this would combine document B page 1 document A pages 1 to 3 and document A page 16 
# into a new combined pdf in the order specified.

Rotate 2 documents 180 degs and combine them

pdftk A=scan0123.pdf B=scan0124.pdf cat A-S B-S output combined.pdf

Rotate whole document 180 deg

 pdftk scan0125.pdf cat  -S output scan0125r2.pdf

PDF Labs Examples
https://toggen.com.au/it-tips/gnu-linux/linux-tools/rotating-a-document-using-pdftk