1) Keep notes as you set it up. Include problems you encountered and what the solution was, develop lists of how to install and configure the various services so you can refer to them should you need to reinstall things in the future.
2) Do it one service at a time and get each service completely running before starting on the next. Your server isn't a single thing, it's a home for multiple things. Do each of those one at a time.
I once joined a company after they ran out of backend engineers and had to restore a server from a backup. Figuring out how to bring all the services up based on history was a fun ride.
This. I still have a 10 year old server setup file that I refer whenever I am setting up a new server.
Later, when you upgrade or modify the service, you can keep adding to this notes.
Also, copy any configuration files OFF the server and into you notes when you are done editing them.
What do you think?
But never too late eh :P