The Johnson/Kelly debate is an interesting one.
We know very little about what Comolli is thinking long-term for the right back position, but I can easily see letting Johnson go in a year or two if Kelly will be kept there long term. We could get a pretty good fee for him if Chelsea or Real Madrid came in for him, and we do have Flanagan as a 3rd option, so it's not like the position would be decimated with his departure. If the links to Isla are accurate, if we could sell Johnson and buy Isla and leave a profit of 6-8 million or so, that might be a good option. Isla could alternate with Kelly at RB and provide cover in a few other positions, which might improve the team. Plus the 8 million could go towards a really top class right winger if we were short on funds for that purchase.
All of this is, as I noted, speculation. It could easily be that Kenny and Comolli see Kelly as a long-term prospect at centre back, and so it would be foolish to think of selling Glen unless the offer was incredible. I still would like to see him played there, as he was very good at centre back for the reserves and might just prove to form a partnership with Coates (or even Wisdom?) that, in 2 years or so, could replace Skrtel and Agger.
In the scenario where Kelly moves over to the centre primarily, we'd probably eventually need another RB unless Flanagan really steps up as Kelly did a few years ago. We might need another player there for a couple of years while McLaughlan develops, but he's another one to keep in mind at that position. Right back truly is the deepest position at the club at the moment, by far.