Problem after update to 2.9.0, mod_fcgid timeout (1 reply)

I am using Piwik on shared hosting (PHP 5.5.10, fast CGI), no access to command line. Trying to updated to 2.9.0 failed at the database upgrade with "500 Internal Server Error". The error log shows repeatedly:

[Thu Nov 13 10:49:39 2014] [warn] [client xxx.xxx.xxx.xxx] mod_fcgid: read data timeout in 45 seconds, referer: http://www.example.com/
[Thu Nov 13 10:49:39 2014] [error] [client xxx.xxx.xxx.xxx] Premature end of script headers: index.php, referer: http://www.example.com/

- according to the URL it was sometimes triggered by the tracking code (I then added record_statistics = 0 to config.ini.php), later by http://www.my_piwik_installation.com/index.php?module=CoreUpdater&action=

The error log shows also sometimes errors:

mod_fcgid: stderr: Error in Piwik:

Followed by some lines of html, inside among others:

Unable to delete merged file : /var/www/ .../tmp/assets/asset_manager_global_css.css. Please delete the file and refresh

Deleting that file (0 bytes) and refreshing doesn't solve that problem.

Any hint how to fix it? Thanks!