Is keeping money in and taking profits from the Islamic Bank lawful? 

If Allah Wills this is lawful, because they stipulate on theselves to work in accordance to the guidlines of Islamic Law. And Alalh Knows Best.

What should I do in order to wake up for Fajr (dawn) prayer?

All perfect praise be to Allah, The Lord of The Worlds                                                                                                                                                                What should I do in order to wake up for Fajr (dawn) prayer? Answer: Some of the acts that aid in offering Fajr prayer are: 1- Going to bed early. 2-  Willingness to wake up. 3- Reciting Al-Korsi verse from Chapter Al-Baqarah. 4- Taking refuge in Allah from the cursed devil, and making ablution immediatley after being awake, but it is preferable to ask someone to help in this regard to perform the Fajr prayer. And Allah Knows Best.

Does ill-gotten money hinder the answering of the Du`a (supplication) and the means of subsistence?

Sins hinder the answering of the Du`a, and deprive the sinner from means of subsistence; whereas, acts of obedience facilitate making a living. Allah, The Almighty, Says (What means) : "And for those who fear God, He (ever) prepares a way out. And He provides for him from (sources) he never could imagine." [At-Talaq/2-3].

After I had prayed, I found a drop of menstrual blood and was unsure when that happened; what is the ruling on my prayer and fast?

All praise is due to Allah, peace and blessing be upon the Messenger of Allah.

Your prayer and fast are correct ,and you should not make up for them, and we ask Allah, The Almighty, to duely reward you for these acts of worship. Your menses start once you see blood because the situation remains as such unless there is certainty or predominant conjecture, as per the Fiqh maxim: "Certainty is not removed by doubt". And Allah Knows Best.