Can a former employee put a stop payment on my final check?

First, contact the state department of labor immediately (which is probably Tuesday, given the holiday weekend): they have the responsibility to enforce the labor laws, including about payment of wages, and may be able to help you.
If they can't or won't help you, you can sue the money: an employer MUST pay you for all the work you did, and failing to do so is not only a breach of labor law but also a breach of contract--a violation of the agreement (even if only an unwritten or oral one) pursuant to which you did work in exchange for being paid. If you did the work, you must contractually be paid--i.e. since you performed your side of the agreement (work) the employer must do his (pay). 
You can clearly sue for the stopped pay. As to the docked pay, if you were paid either your wages OR your salary when you were doing the training, you were paid what you are entitled to. An employer can have you do two jobs at once without having to pay you separately for each. So if you received pay for each day you worked, you were paid, even if you feel that under the circumstances, you should have been paid more. If you were on salary at the time, so long as you received salary for those days, you were paid; if you were on hourly wages, as long as you were paid for all hours worked, you were paid. If not paid as per this paragraph, however, you could sue for the unpaid wages/salary, too.
Your best option for suing would be small claims court, as your own attorney or "pro se": it is not only much less expensive, but it is typically the fastest court out there.
However, even fast court will not get this matter resolved within 15 days. You may need to try to work out a payment plan or delay with your bank in the meantime.