The bottom line is that AA does not offer J between ORD and SJC, only F & Y. For what it is worth, the only J services in the US are so limited as not to be worth discussion in this thread.

The question is what class of service your IB fare bucket books into on AA and that is most likely Y if this is a significant sale. Although nobody can say with certainty without the specific historical information.

One thing you might consider doing is calling AA in the US and asking why it is that your J fare booked into Y and not F. While AA can't touch the ticket, you will at least get a quick answer.

Presuming that AA did not make a mistake here, your options are to accept the Y seat, to pay for the change to F or to take the refund.