The first and last URLs above are done. The other will take some time, because the link to the next or previous chapter is embedded and uses the same label, so it will take some reworking.
I'm working through some of the font issues but it's tedious and I'll get to it as I can.
Thanks.
EDIT: I think I managed to get all the corrections in the S1 material, but I was a bit cross-eyed at the end. Please advise if there are any remaining problems. I know the "TIPH" reference still remains in the "next" and "previous" links, but I can't fix those at the moment.