It does quite literally sound like your valves are out of adjustment. Theoretically, if the valves are grossly out of spec, they could fail to stay open long enough to allow for the mixture to burn completely, or too long which might cause a rich condition. But that probably isn't the issue here. I don't think that this is related to your running problems.

My guess is that your air mass meter is failing. This can result in a rich mixture (fouled plugs, black exhaust) and the surging symptoms I've experienced first hand when I had an ailing AMM.