Where you see documents on where to put the ini file an what not you can ignore that as TunerStudio has the ini and takes care of that as you were doing above.
The Manuals link at the top of the page has an MS1 downloads section. There are still some old MegaTune bundles, but MegaTune is unrelated to firmware installation. The firmware is loaded with the dos program in the firmware zip file. The download you probably want is the one that says "Latest firmware 029y4a only (32bit/64bit)" with this link:http://www.msextra.com/doc/ms1extra/Dow ... 029y4a.zip
Download that zip file, then extract it somewhere.
Then run "download-firmware.bat"
You will be prompted for com port, etc and give some instructions there.