To get it to save, obviously run the comandos.reg to modify the registry. Then what you need to do it add the following three lines to Comando.cfg in the OUTPUT folder:
.SIZE [ .INITSIZE 3 ]
.PROFILE [ .USER 0 ]
After doing that my saving and loading works perfectly.
To get the game to run at the proper speed (the fast speed doesn't really bother me too much, but here's the solution nonetheless), download Advanced Game Loader from here: http://www.sven-of-nine.de/site/doku.php/downloads
Then run that program and go Options -> Add Game to create a new entry for Commandos. Then in the options tab add the Commandos execuable (e.g. C:\Games\Commandos\Commandos.exe) and then at the bottom there's a ticker to choose by how much you want to slow down the CPU. This value will obviously depend on your CPU but it should be easy to get a nice value with a bit of fiddling.