After finally completing a clean install what is the BEST way to replace my data.

Please understand I moved from PC to Mac in Late 2011. Unlike windows where you have to know how it all works to use it, Mac is so simple I, to my own detriment , did not take the time to learn more than just my daily use. Been busy moving country and other crazy life stuff. I am rectifying this mistake. I did have issue with the clean install process working through with out interruption, some file issue, so had to repeat a few times.
1. completed a clean install through to completion of set up, new account etc. Machine runs amazingly better. Completed updates. Knowing Migration Assistant can deal with duplicate user issues.
Q? Do I need to run disk repair or other.
2. Thought myself ill equipped with knowledge and understanding to manually replace my data via finder. I simply do not know where things are supposed to go.
3. Tried reinstall of everything thru set up but it installed everything including all the issues I had before. Went through clean install process again.
4. With this in mind I am hesitant and very weary to use Migration Assistant to move everything back as I simply do Not know where the issue lies even if it allowed greater folder & file separation.
I have got to the stage where I am ready to recover my data which is on my backup external hard drive. The data was recovered using Time Machine.
I wish to do what is best for my machine. It is getting older and I wish to do what I can for its longevity.
Q? So what data is best recovered in which way and in what order.
5. Is it best to say do recover applications from App Store and redo all updates if required.
Then install non app store apps, e.g. Microsoft office for mac, and others thru finder.
Users thru Migration assistant etc etc.
Been learning and working on this since my last post. Lots of watching YouTube and reading for hours.
So much conflicting opinions and maybe this is due to my lack of specifics and most posts are for general use so I do understand.
Again thank you in advance. I still think Mac has it all over PC.

I read thru the data migration one below however wasn't sure of its applicability given it was from 09.
Re: 2. there seems to be data I have yet to bring across. How important it is I don't know. What exactly it is I also am yet to find out. Will proceed with the downloading n stuff.
Thank you for your help on this.

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