With these upgrades, some code may no longer be compatible. If we announce an upgrade has taken place and your code stops working, you may need to research what changed between versions and rewrite the errant code. We do offer as many tools as possible to help troubleshoot code errors. The best being the server logfiles. The are availible via the logs subdirectory of your site.
Chances are, a very helpful error is caught by the webserver and logged.
For more information on using telnet with your Enhanced Showcase account, visit this telnet page. Yes, depending on the FTP application. The best way to change file permissions would be to telnet to the server and change them from the shell. This could take up to a few weeks. Submitting your site directly to them could speed up the process.