I like the epoxy ideas. How would the vertical parts be done?You don't need to start over in my opinion. Fill in the large gaps with small pieces. Build up all the surrounding edges to form a "dam" to contain the epoxy about 1/8" over the highest block. make sure all the small seam are sealed with adhesive like Liquid Nails but do it neatly. The epoxy will find the smallest crack and flow out.
use a clear bar top pouring epoxy such as Blacktail Studios uses. I may require two applications, watch the video to learn the process.
The epoxy will be expensive but you will end up with a far superior finished result over poly.
That would mean losing all the rustic? detail, color and character of the existing boards. It would look like a section of flooring if all the boards were overlaid with new.Another idea:
Instead of replacing the boards which will be a royal pain in the rump, start layering a new layer on top. This time use a table saw and whatever else you have available to make parallel cuts on the boards so that they will lay against each other without gaps.