Most of the communication issues (since that is what they seem to want to call it), have come from the Safety position. All to often the guy jumping underneath routes, and exposing the secondary has been McLeod. Yes, Jenkins made a big mistake on the deep ball at the end of the 1st half. But given they were supposed to be in a Cover 3 zone, the FS cannot jump an underneath crossing route. When the MLB is the closest thing to deep support, it was a total breakdown.
From where I am sitting, the CB play has been the least of the issues with this defense this far. They sell out to stop the run, with McDonald being the guy in the box who makes more plays then the LBs do. The pass rush has been a non factor, mainly due to the fact that teams know they have to game plan to get the ball out quick. McLeod has made a few nice reads, but for all those saying Jenkins "gambles" too much, it pales by comparison to the times McLeod has guessed right and actually made a play.
Getting Johnson back will certainly help, but to say he is the best cover CB might be a case of wishful thinking. One thing that could come of it, is Joyner getting some work at FS while Gaines slides inside to the Nickel CB spot. And while that may be even more wishful thinking, especially since it would mean having two rookies on the field in those situations, it could go a long way in solving many of these issues.