The first counselor at the testing center and the one from Gay Mens Health Crisis (GMHC) were correct. The one in the middle was too conservative. If you'll scan this forum, you will find innumerable discussions about the fact that 85-90% of newly infected people have positive HIV tests by 4 weeks, so your early negative test result is strong evidence you didn't catch HIV from your drug-using partner. CDC and many health departments indeed take the conservative/cautious stance that it takes 3 months (i.e., 13 weeks) to be absolutely certain, but it almost never takes that long for standard antibody tests to become positive.
The odds are very strong your partner didn't have HIV, despite her drug use, assuming she was not a needle-sharing injection drug user. But I understand the value of testing for peace of mind.
In summary, you can be highly confident you don't have HIV and you can expect your follow-up test at 3 months to also be negative. For more information, use the search link to find many detailed discussions; try search terms "HIV test", "seroconversion", or "window period".
Best wishes-- HHH, MD