It seems as if you are saying you cannot do an upgrade of jDownloads if you have a lot of files.
That is not what i says. You can upgrade but you must use other server settings. If this not possible (on server with restrictions) , you have the possibility to do this in a local installation on your PC. Afterwards can this upgraded data moved to the server.
Are you sure that you have read the upgrade instructions in the documentation?
And why will you upgrade to Joomla 2.5 and not to 3.x?
When you will, i can do the upgrade process for you. I need for this case a backup from the jDownloads old data (1.9.x). Created with the jD backup function. And the download link for it can you send me via PM.
By the way, i know a user which has succesful upgraded to jD 3.2 and he had more as hundred thousand
files. But the upgrade process had lasted some hours. So your 300 second setting is nearly nothing.