Welcome to PF!
Send them in, stay the course. These kinds of things always happen and you have keep pushing forward and come up with a plan to overcome any pressing problems. Believe in your self, I was in a similar circumstance once and that was many years ago.
He who hesitates is lost.
With respect to Thermo, I'd also find out why I flunked the course looking at each problem I didn't understand and learning it to learn it. You never know when you may need it in the future. Who knows you might make it to some game show and your deciding question is related to Thermo and you could win thousands or your kids could be suffering through it in the future and your insight helps them through. Also you need to know if its how you study that's the problem as it may relate to other courses in grad school.
With respect to your grad schools, make sure you send in a spread of 3 top schools, 3 you thin you can get into and 3 backup schools. You will go just which one is the question.