After entering the Monastery the sword & noose is supposed to appear in your inventory again as you automatically pick them up. This doesn't happen which would make later puzzles unsolvable. Do they just magically appear in the inventory later?

I've forgotten much of the details now, but back when I was hunting for bugs related to scoring a couple of months ago, I noted about one of the changes I made that "One other positive difference is that with the change, you get to keep the sword after entering the monastery (um1e.scr). Without it, the sword is lost until the end of the game, when you get it back."

I don't remember any other puzzle requiring the rope (which I don't think you get back...?), and I only remember you need the sword at the end of the game, where you magically have it again.

All of the scoring fixes (and thus, indirectly, the sword fix) should be in ScummVM 2.2.0. I don't know which version GOG uses. (There were also some notable fixes in 2.1.0, like enabling support for the high-resolution videos. Though I'm sure things could be improved further with those, because I did see some noticeable interlacing in at least one of them. and getting decent audio volume is a bit of a hack at the moment. But I think it's fine for now.)

GoG version is still using ScummVM 2.0.0 from Dec 9, 2017.
One can download the newest version from scummvm.org site and overwrite the version in the Zork GI install folder. But, note, if you verify or reinstall it will be back on the old 2.0.0 version.
I usually put the newest ScummVM in its own folder on a drive and point it to any games it supports. That way, only one location I have to worry about updating and it won't be overwritten by old versions in GoG Galaxy. Yes, you lose the "time spent" tracking... but I never pay attention to that anyways. I suppose you could update the GoG Galaxy "launch game parameters" custom executable under Configure of each game that uses ScummVM.