Thanks for the through and detailed feedback.
I'm sorry that you had issues with the disable/enable 3rd party customisations tool. Generally we find this to be robust but as with anything in code, it's possible edge cases arise. I'll happily take any logs or information you may have as to way your custom app failed to come back online so we can look for any issues with our code.
I realise it's the "can you turn off your modem and turn it back on again" step is frustrating but when you come onto our side of the fence, you see dozens of tickets a day where something is broken, so we investigate and it sometimes goes through a T1 tech (20-30 mins) then into a developer (60-90 mins) to determine that it's an issue with third party code. This happens daily. In your case with a skilled developer, there's only a slim chance it's the case, but we have to pitch this at the lowest common denominator unfortunately.
We are in a bit of a bind as we're committed to low renewal fees, so the forum app renews at $80/year or just under $7 a month. This doesn't cover a lot of support time or development time, so we really have to make it as streamlined as possible. It's why we're still able to offer email support for our cloud community plans. I would imagine it's why Rackspace are also able to offer support.
In terms of documentation, we do review it but not as often as we would like to. That's a fair comment and I'll review our policy.