Congrats on finally making it! You will be SO happy with your new smile I'm sure.
The Pen. can make your tummy a bit wierd - this is just one of the properties of drugs

. It may help to eat something very bland with it if you are not already. Also, it will probably get better the longer you are on it. Often, the first couple days while youre on a new med and your body is adjusting to it you may feel sick. If it continues, ask if you maybe could get some antinausea meds (or just go get some motion sickeness medication) or maybe try a different antibiotic.
Lots of people do feel better after taking care of a troubled mouth. If you have an active infection, your body is always in its defensive mode trying to cure itself. This does make you feel bad sometimes - much the same reason you feel bad sometimes after getting a vaccination. Your body is in overdrive trying to create antibodies and fight the infection, so it stays run down. Without the infection and a good clean mouth, your body doesn't have to work this hard. It really does make a difference. Also, just the self confidence you will gain will be a big boost!
I hope everything goes very smoothly for you...