Recently noticed that my right foot toes are pointing down some while left foot is reasonably flat. Have had problem with right knee occasionally brushing top tube. Where do I start?

Knees wobbling left and right as you pedal can lead to injury. There are lots of possibly fixes, including better pedaling technique, saddle height, cleat position, etc. All these things can be hard to dial in by yourself. You could start by asking an experienced friend to watch you ride and point out problems with your technique and motion. Once you understand exactly what the problem is, you may want to hire a local coach to work on a fix.

My right knee also tents to nearly brush against the top tube also. My solution was to fill under the foot bed at the arch which caused the knee to travel straight up and down as hoped for. Another solution is a wedge shim between the shoe and pedal. Your bike shop may have such a shim to use in their fitting process.