... usually where I see things like this go goofy is in translating verbal instructions to email. Usually someone very familiar with the process outlines it on paper, and than its truncated for email purposes, which presents three possible problems.
The first is the writer is too intimate with the product and thus can't see the material any longer through fresh "new user" eyes. The second is the person writing isn't a writer at all, and a lot is lost in translation. The third is, when truncating things for email, things deemed not important enough, are cut, and usually those are the things that turn out to be pretty important. ;-)
My suggestions would be to have someone who knows nothing about the product read the instructions to see if they can run through your process without additional help. This could be an editor, or even a family member. Basically someone who is as green-as-green-can-be with your software. The last thing you want is to spend the time to automate your on-boarding only to find things aren't clear, and people call you anyway.
Good luck! Doc