Is what the questioner is suffering from—namely, whispers and thoughts about God's punishment and doubt in faith—considered a loss of faith or a doubt in God, and could it be a whisper that has turned into doubt harming her faith?

You are a Muslim believer, and these whispers do not harm you or affect your faith; rather, you are rewarded for striving against them. Ignore the whispers concerning matters of creed, and say "I believe in Allah" whenever Satan casts any of them into your heart, and desist from such thoughts. If it whispers to you that you have left Islam, pay no attention to it. In matters other than creed, ignore the whispers as well. So, when you perform ghusl, let your ghusl be done once, and do not repeat it. Pray once, disregarding the whispers of Satan, and beware of abandoning prayer.