All Scripture is God-breathed

Recently I read the following verses and have mulled over them many times over the last few years.
2 Timothy 3:16-17 (NIV) All Scripture is God-breathed and is useful for teaching, rebuking, correcting and training in righteousness, so that the servant of God may be thoroughly equipped for every good work.
I wonder if the modern church is honouring Gods word as it should…… do I accept it and follow it in faith or do I need to reduce it to what my human mind can comprehend....
There are many topics under fire now a days such as grace v.s. works, the marriage covenant, and sexual orientation, etc. It would appear that there is a tendency in today’s church to verse pick to suit the situation, to gloss over what are deemed secondary items, to refer to some of the bible as cultural and not applicable in today’s age and so on. What I keep asking myself is, if I consider certain scripture irrelevant to today, what am I reducing the bible to? At what point does the reduction stop? Does it undermine the bibles integrity? If I say that I am a follower of Christ and his word (bible) is my guide, how does a non-Christian respond if I reduce it to what I think makes sense in today’s world? I would think that my faith would not be very attractive if I imply that a portion of my guide book (road map) that was “God-breathed” is not applicable.
A wise man commented to me that it is critically important to hold the different scriptures in proper tension, i.e. grace vs works. I have found this to be critical to my bible study along with seeking Gods direction in prayer as I study his word, asking him to reveal to me his direction in my life through his “God-breathed word”.
Don’t get me wrong, I am not suggesting that there are not differences in today’s culture vs that of the bible times, but is the modern day church honouring God’s word as it should aspire to? Are we putting too much of his word in the bucket labelled “applicable in bible times only” and not enough in the bucket labelled “applicable for his children and is useful for teaching, rebuking, correcting and training in righteousness, so that the servant of God may be thoroughly equipped for every good work”.