My girls have SpA and both have had positive ANAs. A weakly positive ANA can be caused by biologics -- your rheumatologist would probably know more than your GI about that. It's not unusual to have a weakly positive ANA caused by being on Remicade.
However, generally you do NOT need to have a positive ANA for AS -- in fact, one of the features is that it is "seronegative". It is much more common to have a normal ANA.
HLA B27 is the main gene associated with AS/SpA. Something like 90% of caucasians with AS have the HLA B27 gene. The likelihood of being HLA B27+ with Axial SpA (the earlier form of the disease) is lower -- something like 60% if I remember correctly.
Any joint can be involved in SpA/AS -- including the hands and knees. In some people, joints flare when the Crohn's flares and in others, it is completely independent and has to be treated as such. My daughter is one of those people -- her Crohn's responds beautifully to Anti-TNFs but her AS definitely does not.
Charlotte is right -- MRIs are a much better tool for diagnosing SpA. Damage can take 8-10 years to develop (though it can certainly happen faster) and until then, x-rays would look normal.
Disc issues are unlikely to be related to SpA.