First, be thankful you chose to use protection; I hope your future STD/STI test results show negative for HIV due to that decision. I always have a very frank and honest discussion with any partner about sexual health before becoming physically involved. However, even results can be fabricated, if the liar is determined enough.
Second, I feel for you. Unfortunately, it sounds to me like drama surrounds this couple. They admitted being new to poly, and I feel like Bob has major jealousy and insecurity issues that became inflamed when you were more emotionally involved with Jay. It seems that often couples experiment with non-monagamy when their relationship begins to break down, and you pointed out already that this is likely the case with Bob and Jay.
As for your emotional health, I know you are hurting now and your body may be irrevocably changed due to your relationship with Jay, but I would recommend you make a clean break of it. From what you have said and what I have seen and read before, this will not end well at all. Jay has chosen the relationship he has with Bob over the potential relationship he could have with you. I also find it completely unforgivable that Bob lied about their sexual health; you cannot start a constructive relationship on lies, especially ones of such magnitude.
As for your sexual health, I would get tested immediately and again three months from now. I really recommend that you abstain from sexual contact with others during this period. I am not a doctor, but two consecutive negative tests separated by three months should give you enough comfort in your health to resume activities and regular testing schedules. Please, medical professionals speak up here; I too would like to know more facts.