The clay pockets are easily explained. Rivers as you probably know, are very mobile. By that I mean they flow across the width of their flood plain to one extent of another depending on the life cycle the river is passing through.

Ir maybe that the river channel was once the site of a braided channel.

Clay beds are made up of a deposit of fine particles as you well know. To accumulate a thick body of clay, it is necessary that muddy water, water with clays in suspension, be allowed to settle out depositing the clay.

So in order to deposit clays you have to start with water carrying a substantial suspended load. They you have to provide an area where the water is trapped where it becomes still allowing the sediment to settle out.

I can envision several cases.

First you have a braided channel. At higher brief flow rates, the water picks up a large suspended load and fills some of the secondary channels. The flow subsides, leaving some of the water trapped in the secondary channels, they could be old meander cutoffs, The water sits and settles depositing its load. This happens over and over time accumulating more and more clay.

Another case is the river broke its levee and the resulting breach allowed clay carrying waters to spread out, and stand depositing its load. Later the river meanders out of its old course and the new channel the one you are working on, is standing over the old deposits of clay that were once on the flood plain.

A third case would be where a change in the river gradient, due to sea level change has caused the river to advance over what used to be an old flood plain. The clays you are seeing would have been deposited where the older river entered into a body of water, lost energy and deposited its load. Subsequent drop in sea level, caused the river to advance over the old delta deposit.

The last case seems unlikely since it sounds like your location is inland. My best guess would be the braided channel scenario, or meander cut offs.

If you can get a good clean exposure, by that I mean go in with a knife and shave the face of the cut to remove the marks of the heavy equipment, you might be able to see very subtle bed forms. I would expect that there would be very fine layering in the clays if they were deposited over repeated events. If not, then they were deposited in very thick layers all at once indicating a tall column of load carrying water.

The silts should also exhibit some bed forms, like fine angular ripple fore sets indicating the direction the water was moving. Think of the angular foresets as the front angle of a ripple similar to this:

\\\\\\\\ -> being the direction of flow.

I would be interested in knowing the location or climate that you are located in. That would provide a bit more information with which to refine my answer.