Backup Drupal - Ubercart on HostMonster

After testing the Drupal backup modules such as “Backup” Backup Files” “DB Maintenance” Backup and Migrate” and “Backup Server Client” which I found the best, due to the fact I could back up my site and remote sites in complete form, until my site backups started to fail due to “MySQL server has gone away” “Cron has been running for more than an hour and is most likely stuck” plus Attempting to re-run cron while it is already running” errors.

These issues started to occur once my site data reached around 100mb when compressed. My database is less than 3mb when uncompressed.

I would have thought that I could backup a much larger site without running into limitations. My site will be around 300 – 350mb once all my products are loaded.

These issues have led me to look for alternative approaches, so I read through forums etc. I am still at a loss to understand why these errors occurred.

It appears that it could be a php limitation, which could be related to the Drupal / Module and or it could be a host limitation, as I am on a shared environment.

1. Are these issues Drupal / module related or are they host related limitations?
a. Can anyone enlighten me as to where these failures stem from?
2. Do these suspected limitation exists if running bash scripts via cron or similar.
a. I believe that using bash scripts by passes any php short falls.
3. What is the best way to backup everything – Data and database for each site?
a. Possibly such as Drupal.org would use.

Thanks for reading this post and leaving your input.