1) you can't create TOC with makelrf (it's a separate object from the text).
2) pylrf doesn't need a source LRS. It can generate one though.
3) if you use Book Designer to create an LRF book, you can find the source LRS in its "temp" subfolder.
4) you can decompile most LRF books with lrf2lrs.py.
As for LRS reference, here it is:
https://www.mobileread.com/forums/showthread.php?t=8795