Hey there pal,
I'm sorry this has been so hard on you. I can't tell you what's most likely the cause of your symptoms (or your girlfriend's), so anything that worries you will need to just be evaluated by your doctor.
What I CAN tell you is that all of the cancers you mention are rare, rare outcomes of any HPV infection, and when they do happen are virtually always related to "high risk" types of the virus that aren't linked with warts. Oral cancer, for example, isn't associated with warts and typically takes 10 years or so after exposure to develop.
Similarly, warts don't cause penile cancer, and this particular cancer usually has an "early" lesion called Bowen's Disease, where the skin has a superficial malignancy that is often treated on an out-patient basis.
In another post of yours to which I responded today, I chatted a bit about anal warts in someone with no history of anal sex. Read it by clicking http://www.ashastd.org/phpbb/viewtopic.php?t=5285
I hope this helps. Again, get any symptoms checked out to see what might be happening (if anything), and if your doctor wants you to do something. Let us know, ok?