We face this problem as well. We are working across multiple systems and sometimes unable to take advantage of the various triggers/reports etc we had setup in our own JIRA, which meant we had to work harder to deliver to the same standard.

So, we developed a robo-advisor to deal with it called stratejos (http://stratejos.com). stratejos takes care of house keeping (like making sure the tools are being used as expected) and provides project analytics on top of this. We're currently in beta, would love to hear the problems people are having so we can solve them.

With the skype/chatting/etc this is probably something you just have to deal with, as someone else said, its part of being a consultant.