My advice is to wait until they give you an offer, before you fire a list of questions over to the Hiring Manager by e-mail. Because, if they don't want you anyway, then you will be wasting your time and these questions will be academic. Besides, they might offer you another interview round, in which case you may yet get a chance to ask your questions in person.

If they do give you an offer, then you can write an e-mail to the Hiring Manager, stating that you like the position and think it is a good fit; however, you have some questions that you would like them to answer, before you would accept.

If you think they are disorganized and want to withdraw your application because you are put off by what you have seen so far, that's obviously your choice and you should probably do that, if you feel a strong aversion. However, seeing as they have yet to make a decision, I personally would keep the application in there; keep my options open and see what happens. You don't have a lot to lose by doing so and you can always turn the position down at a later date. Once you have withdrawn, there is no going back.