I think most of your troubles should be improving. many couples fight or marriages are difficult in the first 3-5 years. You both have a son and we don't know the jobs of both of you.
The first step to any happy marriage is understanding each other. Have a discussion with your wife, involve close friends if needed and then family members on both sides. I think there would be misunderstandings on both sides.
Both of you list out (write out) the issues that seem to make the marriage difficult, be frank and honest in this aspect.
Try to analyse about her ambitions, desires or expectations from married life, from you and from our family.
Analyse if there is any unresolved emotional issues on both sides.
Do not confornt her directly that she's a lair,try to find out why and the motives behind it.
If you find some answers like, she wants to be employed, change a job, then help her in this endeavor. If she feels that she has to be independent, then give her that within the degrees of commonsense. If she feels that she should have a separate home than staying with your parents.The have a chat with your family and try and see if this would be possible.
Focus on your son and try to spend more time with your son and wife by travelling, visiting places and improve the family bonding.
Both of you can seek the advise of a counselor to guide you through this difficult time. You will find that things get better. Then continue with your efforts to keep your married life pleasant.
If both of you believe in the Almighty, then spending time at places of faith will certainly help you.