The other day an atheist was trying to argue on youtube about a few scientific contradictions in the Qur'an and using one example where he said the Qur'an is innacurate in saying that semen comes from the backbone and rib bone as chapter 86 verses 5-7 state... However, I realized that there is deep meaning behind these verses and I must research them, in the process of researching someone said the backbone's job was to produce semen and I said this can't be true, however I later found out that it's not talking about production but rather PROCEDING from that patricular area.... Aka the epidiymis... Now during this whole situation I felt a very uncomfortable feeling inside of my heart... I felt like doubt was instilled in me and I hated it... And I know they say this is the work of shaitan, but is it true that shaitan can make it look like it is you doing comitting kufr while you're really not? please help, i'm afraid i've lost my good deeds because of this... I researched the situation to get a better understanding and felt very nerve wrecked and scared from this doubt that I tried to get rid of... Please help.
First, you must know that the Qur'an is book of guidance, and the guidance that is in it makes it a miraculous book which can only come from Allah(swt), this is all u need to know about the Qur'an, follow its guidance.
Since u believe in the creator Allah(swt), he couldn't have left the creation without guidance, when u search u will find the best guidance in the Qur'an. Now about science, the solution to your problem is by remembering that our knowledge is limited (no matter how sophisticated or scientifically advanced we have become), always keep the door open to the fact that Allah knows best and that our limited minds and senses might not have reached full knowledge about a particular phenomenon etc.
Second, don't forget that the Qur'an was NOT meant to be a manual about scientific facts, it is for a greater purpose, the message is relevant for people of all ages and times, back from the primitive beduoin arabs in primitive ages till our modern times.
Finally, i can assure u that a lot of people have been in your position including myself, this period of doubt isa will go away. Have faith that Allah(swt) will heal u, take this an opporunity to fix all your mistakes, avoid sins, be regular in your prayers, kind towards your parents etc.
Finally, if the atheist wants to argue, respond to him by the argument of the Quran in a particular incident (maybe someone can quote the full ayah) "bring me a book that has guidance better than these two (torah and Quran) and I will be the first to follow them".
A true believer is one who's fitrah(natural inclination) is clean and will feel peace when following the guidance of the Quran
May ALLAH(swt) give u guidance and let your heart be at peace.