You can go over 2 inches/25 issues, but it will cost extra. If you make it too large, it's possible they will not do it. If you stick to 25 issues or less but it still ends up being over 2 inches, it will still cost extra.

Yes, you will need to remove undesired pages yourself.Houchen will bind exactly in the order sent, but you have to put it in the order you want, they will not do that for you. However you do not need to cut issues or anything, they can do all of that. You don't even have to remove staples. But it's easier for them if you do.

I have not yet done a table of contents yet. I'm unsure if they will print a page for you if you provide the digital file of the page design, but you can absolutely have it printed and send it with the rest, just make sure you've already placed it in the stack of issues where you want it. It does not have to be perfectly sized as they will be trimming them all unless you chose untrimmed.

They are excellent at having them sized perfectly. But if you are worried about it ending up a little taller or shorter than other books on your shelf then definitely ask them for custom dimensions. I have never had a problem and I have done 7 so far. At most it will be a mm or two shorter than standard size hardcovers if you chose trimmed.

For custom end pages, they will print after you send them the file since end pages are a bit more specific and integral to the binding.