Craig,
Congrats on completing the project! What happens to the track-hoe now? Having done this project, would you do anything differently? Maybe too soon to ask that.
I'm finally successfully getting necessary equipment lined up for the construction of Ponds "X" and "Y" very soon. Any thoughts you may have on the track-hoe's utility would be appreciated.
Regarding repairing the dam area, my approach has been very similar to yours and has always worked for me. I use a tractor w/front end loader loaded & back-hoe to drive over the area repeatedly...that in addition to the dozer does the job for me. (Edit...I also feed range cubes to about 30 cows right over the spot

)
I've never used bentonite personally but have researched it considerably. My thoughts would be it isn't necessary in this case, but it may offer some cheap insurance and make you feel more confident that you've done everything you can to properly restore the integrity of the dam.
I noted with interest and some concern your comment on the soil removed not being clay. However your description sounded like clay and if it wasn't leaking before, it shouldn't leak now either...assuming you are very careful to not inadvertantly mix in some sand in the process.
Congrats again...nothing like the great feeling of a project successfully completed. Like Hannibal used to say to the "A" team, "I love it when a plan comes together"!