The easiest solution is to interface with the site through some documented API that bypasses the Javascript. But this would mean that you've got explicit permission to be doing what you are doing. If nothing of the sort exists, it's possible that the bank has no intention of allowing such activity.

In any case, you ought to secure that written permission before you proceed much further. Without explicit permission, in writing, you're probably running afoul of the bank's website's Terms of Service. I think that scraping a bank's website is at minimum going to earn you a cease and desist letter, or worse.