Oh sweet lord, I'm sorry for the care you've received.
What tests were on the 7 panel test?
Even if the RPR was negative, this could still be syphilis, though it doesn't fit it perfectly. Healing in 2 weeks would be on the short side, but developing at 5 weeks is in the proper time frame. Most people will test positive by 6 weeks, but some can take longer, up to 90 days.
Have you googled syphilis chancre sores to see if yours looks like them?
It could be herpes, but again, it doesn't sound like it. Herpes sores are blisters, not really "open sores", and don't start out as anything that resembles a pimple. I'm not sure that herpes was included in your blood work, but look for something that says, "hsv1 hsv2 IgG", or something similar. It can take up to 4 months to test positive for herpes.
Was any of your encounter protected?
Did your doctor culture the sore? That would have been the best way to determine the cause, since it could have been an infected hair follicle, a staph infection, or a variety of other things.