Having been 100% remote for the last 5 years, I feel I can comment here.
I'm a little puzzled by the first few items in your list... I work at a pretty big company, so maybe that is why. Specs are a way of life where I work. I would hope that everyone would be good or learn to become good at writing useful precise specs.
Accurate and concise emails goes without saying.
I would agree with the body language from written communication if you never spoke with anyone on the phone, but that would be pretty unusual I think.
Web-based meetings, virtual whiteboards, are fantastic. I'd much rather do web based than sit in a conference room.
I don't really have work relationships anymore, but it's not a loss. More of an exchange for relationships outside of work.
The water cooler comment I agree with. I don't have the "pulse" of the human terrain anymore. It bothered me when I was losing it, but I don't mind anymore.
I used to worry about the "being included" part, due to the out-of-sight, out-of-mind effect. I have to be more of an advocate for myself than perhaps I otherwise would. However, my work speaks for itself, and people want me on their projects. I keep in touch with various project leads and let them know what my availability looks like. I don't feel like I'm missing out.
All that said, I worked at my company for close to 10 years before going remote. That was a big help. I personally knew everyone I was working with for the first couple years. Turnover has changed that.
Working remotely requires discipline, perhaps more-so than working in an office. For many people, the commute to work and being in a different environment helps them shift state of mind into a "work" mode. That is harder to manufacture working remotely.
You need to be more available when you work remotely. When someone calls you in an office and you don't answer, they think "oh, maybe they were taking a break or in the restroom". When someone calls you and you work remotely and don't answer, you worry that they will think, "Is this guy really working?"
For the first couple years I worked remotely, I made sure to answer the phone whether I was on lunch or break or whatever. Now that my reputation as an effective remote worker have been established, I don't worry about it so much, but I do still think about it.