Here is a quick description of how to use saupgrade. If you have any questions or problems, you can send mail to firstname.lastname@example.org. I won't always have a solution, and I can't promise an immediate response, but I will try.
If you run into a problem when playing a game on a converted database, make sure you attempt to reproduce it on Steve's example game. Only if you can reproduce it on a non-converted database is it safe to pass along to him.
Tech system changes are not translated. If you have new tech systems in a version which supports saving and reloading use that before translation. Otherwise, you are out of luck. Sorry.
Large history logs will be truncated, as well any very large messages
In the V3.8 to V3.9 upgrade, any existing CFN Tasks will be cleared. The extensive improvements that Steve has made would make it difficult to safely copy over old CFN Task data.
In the V3.95 to V5.0 upgrade, Steve now calculates shipyard complex capacity by specifying a fleet for each shipyard complex. Since this information wasn't in the old database to move over, saupgrade randomly chooses a fleet in the same system and assigns that to the complex. It will likely guess wrong, so you will most likely have to set these yourself