Chris, congrats on completing your first job! It's amazing how much you learn by going through the whole process. I also look back at my first job and now realize how I could have done things better. Hey, you have to start somewhere.
I'm giving you a link to a discussion last week on a problem with grout coloration. You might want to try some of the things the pros discussed before ripping out all of your grout.
If you can salvage your job by one of their methods and the thinset issues still bother you, Dremel makes a grout removing bit in two sizes with a little gig that holds the bit at the correct angle. The good news is that it works well. The bad news is that each bit costs $10 and it will go dull after about 6 linear feet of cutting. Keep in mind that you need to make 2 passes to get all of the grout out of a 1/4" grout line and you can do the math. Really pricy way to do it. However, the Dremel method is great for cutting out small sections of grout to regrout those areas where the thinset shows. Also keep in mind that it is possible to have the Dremel get away from you and scratch or chip a tile. I had it happen once. Keep in mind that the solution could make things worse.
Good luck and let us know how it goes.