Kind of difficult for me to tell from your picture if the plant is planted at the correct level or not, but it would be easy to mound more soil up around the lower stems to get them deeper into the soil.

Being late in tying the plant up should not have caused any issues with your plant. If the plant was sitting in soil that was too moist would have been a problem.

The plant is looking worse now because it was just dug up and replanted. A clematis that is recently dug up often sulks for a while until it gets reestablished in its new site. Make sure to mulch the plant well, keep it well watered, and if it were me, I would prune the top growth back by at least half so the root system does not have to support as much top growth until the roots get reestablished.

I will mound it up and mulch it. I will prune down to the lower set of leaves and hope for the best, thanks.