Hi Bryanna,
Have been reading your advice to many people and finding it helpful, hope you can help me with my specific problem (or if anyone else has similar experience and advice).
I am a mid 30's female with what I consider above average health. I have never had the flu, I get a cold about once every 5-8 years, I eat very healthy (no sugar, no grains, plenty of veggies and healthy fats and proteins), and avoid prescription drugs like the plague. I had a root canal done on my #22 tooth about 10 years ago due to a dens en dente situation that was causing the gum in the roof of my mouth at the root of the tooth to get infected. I remember going to an oral surgeon and getting a curettage prior to the root canal. The tooth was always a bit sensitive even after the root canal but all was good for about 7 years. Then in 2010 it got infected again and the root canal was retreated. I went to an endodontist the second time and was hoping the problem was solved once and for all.
In Feb of this year the area around the root of the tooth became infected again. The pain was not too bad but I knew something was wrong. I went to my dentist who put me on a 10 day course of amoxicillin and told me the tooth should be pulled. I am very skeptical of medical professionals in general and wasn’t convinced the tooth had to go since it had never had any decay and seemed to function great. I was also very attached to it given that it is a front tooth and I saw extraction as a last resort option (once they pull a tooth it is gone for good). The infection cleared up very quickly after the first few days of amoxicillin course and I was determined to boost my immune system and get my body resisting any subsequent re-infection of the area as best as I could. I was oil pulling with tea tree oil and flossing religiously to try to get the area clean.
Two months later in early April the infection came back and this time with a vengeance. I took a second 10 day course of amoxicillin which took about 5 days to kick in during which time the gum on both sides was badly swollen and I had intense pain all through the left side of my head (T3’s every 4 hours for 3 days barely putting a dent in it). The swelling on the inside of the gum went away quite quickly but the swelling on the outside of the gum above the tooth persisted for a long time with a big red ‘boil” evident. I could also feel tenderness on my face right up to my nostril so I knew the infection had traveled a long way. I was on the last day of the 10 day course and was worried that wouldn't be enough to clear it up properly. I went back to the periodontist for a followup and he gave me a “just in case” prescription of clindamycin. I waited a day or two using oregano oil and garlic on the gum (and taking it internally) and was happy to see the swelling and infection seemed to clear up so didn’t fill the prescription. At this point I knew extraction was my only option.
Two weeks after I finished the second course of amoxicillin (1 week ago today) I had the tooth pulled by a highly recommended periodontist who seemed to do a good job. He cleaned out all the infected bone tissue and put a bone graft in right away. He said the hole was quite huge but that the lower part of the bone around the jawline was still intact and all should heal well. He put me on 900 mg clindamycin for 7 days which I was very reluctant to take after just two weeks on the first course but did since he said it was very important to avoid infection from the graft. The next day I woke up and some of the bone graft material was weeping out of the wound, more troubling I noticed the same red boil just like I had when the tooth was infected on the outside gum above the tooth. The extraction site itself seems to be healing quickly but when I saw him yesterday to get my stitches removed and showed him my concern regarding the swelling above the gum his answer was YET ANOTHER course of antibiotics, this time amoxicillin for 7 days. I am VERY hesitant to take another course after just finishing the clindamycin yesterday (which gave me stomach pains every time I took a pill). I have been eating lots of yogurt and so far don’t see any side effects from the antibiotic (other than stomach pain) but I thought the extraction and cleaning of the necrotic bone tissue was supposed to solve things, what’s to prevent more and more re-infection in the future if I am still taking antibiotics a week after the extraction?

So my question is:
1. should fill this amoxicillin prescription or wait a few days and see if things clear up? I am very concerned about doing lasting damage to my gut flora. I took my last clindamycin pill last night and already the area is less tender and less swollen then it was yesterday when I saw him. Will the antibiotic work better if I attack it right away or is it okay to wait to see if I can avoid it altogether? Will the antibiotic even work? I read that bone graft regions can't be targeted by antibiotics anyway since there is no blood flow to that area until it gets incorporated as your own tissue.

2. how will I ever know if the infection is truly gone? from what I have read and what the dentist told me the area was likely infected for some time and there are typically no symptoms. I never had drainage so what happens to the bacteria in between antibiotic treatments...are they just waiting dormant ready to attack again? Does this mean he didn't clean all the tissue out properly? I am due to get an implant in 8-10 months but don't see how I am any further ahead than I was with my real tooth if the area in the jawbone remains infected?

Thanks you all in advanc for any advice you may have!