At day 34 I got tested for Chlamydia, Gonorrhoea, Hepatitis B and C, HIV, Syphilis and HSV1/2. All negative.
I got tested again for the above minus HSV1/2 at day 46. The HIV, Syphilis and Hepatitis B results were negative. Still waiting on others.
 
My concern here is syphilis.

1. I noticed a small spot halfway down my shaft about 6 to 6.5 weeks after exposure. Cannot remember exact date. Could have been a couple of days before my 46 day test but could also have been the day after. It was a small papule that I scratched away at the time but yesterday on day 51 I noticed after a shower that it was red and slightly raw. It does not look like an ulcer nor is it raised like a bump or papule.  It’s about 3-5 mm in diameter and flush with the skin. Today at day 52 the edges have become flakey and it looks like it's peeling. I have left it alone. Could this be an atypical chancre?

2. Could the Flucloxacillin 500mg 4 times a day for 5 days that I was prescribed at day 6 after exposure delay a syphilis chancre to 6 to 7 weeks after exposure?

3. Could the antibiotic also impact the conclusiveness of the 46 day test? Do I need to be tested again?

Just to add the spot now has a covering that looks to be peeling but as I said I've left it alone.

Welcome back to the Forum.  I'm sorry you are having trouble moving forward following your virtually no risk exposure.  You need to believe your test results.  The average time to development of syphilis lesions is 21 days.  In the most unlikely circumstance that you were exposure to syphilis, the floxacillin would have either entirely prevented syphilis or your test at day 46 would have been positive.  Thus:---

Thanks for your reply doctor. I had expected to move on after the negative results but the appearance of that spot threw me for a loop. The spot has now peeled off but is still closed with skin and not raised. Just looks like a round discoloured patch of skin. Based on your advice and since the spot does not look like a chancre I will move on and not test further. My results at day 46 are completely conclusive with no confusion due to the antibiotics, correct?
If I had been exposed to syphilis and the Flucloxacillin prevented me acquiring it could I have passed on the infection to my regular partner in the 6 day period in between my exposure and starting the Antibiotics? Are people non infectious during the incubation period?
My research has suggested that direct contact to a lesion is required for the spread. Is that correct?

You are correct- direct lesion contact is required for syphilis transmission.  The infection is not transmitted during the incubation stage.  There is no risk that you acquired syphilis and transmitted it to a partner.  ---

It has been mentioned on this site that tests should be believed over symptoms and I want to do that and move on. However, since I can't remember if these symptoms started before or after my day 46 blood test that's been difficult.

I have read two threads on this site where it had been indicated that antibiotics could confuse things and delay a conclusive test. I am trying not to be repetitive but can you please confirm that my day 46 test is conclusive regardless of the penicillin type antibiotic I had to take from day 6 to 10? Your opinion will help me disregard the worries of syphilis.

The red spot that I have been concerned about now is just a small patch of flakey discoloured skin. Lighter than the surrounding area. If I stretch the skin I can barely see it sometimes. Is a chancre quite noticable? Is a chancre always an open sore?

Thank you for your expertise in advance. After your responses to my questions above I hope to not need to use your services again.

I have just received all my tests results from day 46. They were all negative. I assume from this point on I should believe these tests and not any symptoms.

This long after your exposure, a day before or after the appearance of the lesions would make no difference.  Further the improvement of the lesion you detected is further evidence that this is not syphilis.  Your results, including the ones that you just got are conclusive.  It is past time for you to believe your tests and move on.  No further testing is needed.---