I've recently begun to truly read scripture, the more I actually read the bible the more faults I find with the church.
Not to be overly cynical, but you'll have that experience no matter what church you find yourself in. Churches these days are not built to house disciples of Jesus... not really.
My father is the most important man in my life and he probably always will be. How do I discuss these issues with him?
Respectfully and with love. The chances of a your father changing his opinion because of anything you have to say is real low. Then again the chances of him having you burned at the stake are fairly small as well. His reaction will be somewhere between these two poles.
I do not want to watch my father follow the false voice of God as the church decides to portray him.
"Wives, in the same way submit yourselves to your own husbands so that, if any of them do not believe the word, they may be won over without words by the behavior of their wives,
2when they see the purity and reverence of your lives"
I know this passage is about husbands and wives, but consider that the power dynamic is similar. You are the lesser and he the greater. If you win him over, it will not be with
discussion. It may be, however, with your purity and reverence, in silence. And... you know... prayer and fasting.
I want nothing more than to please my father but at what point should I follow God the proper way. Should I obey my father's wishes and follow God in a false way but loyal to my father? Or is it better to follow God properly even if the price is disobeying my father?
I know this one. Honor your Father and Mother, that it may be well with you, but do not call anyone on earth 'father,' for you have one Father, and he is in heaven.
You owe your father all duty and respect and honor, but your relationship with The Father is your own. Nothing is more important or vital..
That being said, be certain that whatever you do is what God is calling you to do. I have no love for the catholic organization, but then again I have no real connection with any other brand or flavor of Christendom. I have become quite the hermit, and this is due in large part to my being obsessed with what is proper for a group to do. Being a part of a group that is doing things improperly is not necessarily the same as being told to depart from them. Remember the words of Jesus to the 7 Churches of Revelation: Some of those Churches had incredible problems but I don't recall Him telling anyone to depart the Church they were in, but to repent and to hold fast the good things they were doing.
Which is to say, follow God properly, but be sure what you're doing is God's specific will for your life. We humans like to jump the gun a lot and do what we believe to do God's will based on a lot of presumptions. Fast, pray, and seek the will of God in your circumstances before doing anything drastic.