Well, lacking physical evidence, such as signs of force, rough sex, a struggle, swollen wrists and bruising consistent with pinning a person down against their will, scratches across your face, torn clothes, no use of protection etc. credibility can certainly play a strong roll in deciphering the truth.
However, one big question is what does the girl hope to gain from setting you up? Are you incredibly wealthy? Did you once date this girl and break her heart? Does she have some grudge against you and/or your wife? In other words, if she is lying and taking the lie this far, what do you suspect would be her reason for this? What is she hoping to gain by this deception?
What is your relationship with her and where did this alleged rape take place?
When you had this consensual sex, at what point did it turn ugly? Did she finish her part of the encounter with a smile on her face and smoke a cigarette or did she suddenly turn into a different person just before the fireworks started?
How about your criminal history? Have any assault or sexual allegations/charges in your history? Alcohol or drug related troubles? Domestic violence? Mental health issues?
Did she go to the hospital immediately after your encounter? You claim that the detective picked this case up six months after the fact, but you also claim to have given them the clothes you were wearing that night. So when did they request your clothes? Were they already washed? When did you have time to confess this incident to your wife if they were there asking you questions this same night? What proof do you have that her story has changed? Could it be changing because she was heavily intoxicated at the time you saw the green light?
How intoxicated were you that night? Were any sex drugs involved, like Ecstasy?
As was already mentioned, if she had her blood taken and was found to be heavily intoxicated or drugged, she could claim she was unconscious or unable to resist and you were aware of this fact. That is a hard hurdle to get over, especially if you are much older than her.
What type of case was it you claim she filed a false police report in and is it something you can prove?
All of these things will come to light at trial. But in my unprofessional opinion, her motive for lying is what you're attorney needs to establish. Without her having any motive to harm you, I'd say try to make some sort of plea deal.
You can also expect her to look like the virgin Mary with a good supply of alligator tears while the DA keeps supplying her tissue to wipe them away while speaking words of comfort, telling her to take her time and apologize for how sorry he is to make her re-live the nightmare all over again. So you may want to practice a little crying yourself.
Bottom line, you need the best attorney money can buy and you need the best investigator money can buy and if she's making this all up you need to find someone she has spoken to about the experience.