If you did any customazation or made your own plugins you will have to upgrade those yourself.
In order to upgrade from 4.1 to 4.3 you have to replace all the code. Get the source code for 4.3, you dont need the 4.2 code. I usually delete all files in the project(except what's customized), and then I paste the new code into the solution. This way your sure old files which isn't used anymore is removed.
After that I upgrade everything I've created plugin by plugin. This is usually quite time consuming.
When that's done, and your solution is building, you have to upgrade the DB with SQL scripts. You can find them here: https://github.com/nopSolutions/nopCommerce/tree/develop/upgradescripts
You have to execute 4.1-4.2, 4.2-4.3. They can take a LONG time.