Amumu can also build Everfrost (If you haven't already checked that out, try it!) which gives him a ton of utility. Having Everfrost available more often feels really nice.
Both Ultimate and Treasure hunter subrunes work well, indeed. I really think this is a matter of preference. As you become more adept with Amumu, you should get a good idea of what subrune here works the best. I'll look into adding a little paragraph about these options in the guide!

I've not tested anything so I can't say for sure. Based of my observations,
I don't have any comments on Demonic Embrace, it's probably worth waiting to see.
Abyssal Mask will really only be a buy into AP teams. I don't think the MR debuff is going to be strong, the number is not mentioned.
FoN should become significantly stronger with priority.

Also, Cosmic Drive should feel really good for Amumu's AP build, even though he's not a fighter, the MS should help so long as it stays 30%+.

Hey! I only filled out the threat levels for junglers, and as far as to my knowledge, Syndra is not a jungler. 130 champions would not only be overwhelming for me, but the readers as well! Gargoyle's is a great option against Syndra, and playing against Syndra is about timing. If she casts her E, make sure your Q is ready right after that, her E has a relatively wrong cooldown. You can swap Conditioning and Unflinching (see below) for each AP matchup, but shouldn't matter as much as you're not going to lane directly against them
CC? You can take unflinching!
Against a cho'gath ulti, it's insanely hard for him to even get to that on a champion. As long as you don't Q on him at low health, you should be fine.

If you have any other thoughts or if I haven't answered one of your questions please let me know! Thanks,
ak521.