What are some Simple Steps you can perform to try to fix your database issues?

You can run a repair on all your databases. In the cPanel, click on the MySQL Databases icon and in the Repair section, choose a database to repair. You can safely run a Check and Repair routine on all of your databases.
You can try to optimize all of your databases. In the cPanel, click the PHP MyAdmin icon. On the next screen, choose a database name from the left side column. When the tables appear on the main screen, scroll to the bottom and click the link "Select All". Next, use the drop-down menu, and on the bottom, choose the "Optimize" option. You can do this optimize routine to all of the tables in all of your databases.

Performing these two simple steps will not harm your important data as these steps above are non-intrusive maintenance routines. As such, they may not fix the core issue as well. For instance, if you have severe data corruption, it can cause your queries to time out before they fully execute. Data corruption can be difficult to detect, and repair. Database corruption can occur if a database operation did not completely succeed. Partial data is a form of corruption which can break Referential Integrity, causing your web application to fail also. In short, the free Repair or Optimization routines that I just mentioned may not be sufficient to fix severe database corruption.

# Thu Apr 12 09:02:38 2012
# Query_time: 1.586508 Lock_time: 0.001055 Rows_sent: 1 Rows_examined: 1
use livingci_livingupdated;
SET timestamp=1334242958;
SELECT message FROM uc_store_footers WHERE path_hash = '92fd05d8ffd92d564bac616903a6c8bf'

# Thu Apr 12 09:36:23 2012
# Query_time: 6.502032 Lock_time: 0.008239 Rows_sent: 0 Rows_examined: 29479
use livingci_livingupdated;
SET timestamp=1334244983;
SELECT t.word AS realword, i.word FROM search_total t LEFT JOIN search_index i ON t.word = i.word WHERE i.word IS NULL

# Thu Apr 12 09:42:37 2012
# Query_time: 1.019890 Lock_time: 0.000092 Rows_sent: 1 Rows_examined: 1
use livingci_livingupdated;
SET timestamp=1334245357;
SELECT n.nid, n.type, n.language, n.uid, n.status, n.created, n.changed, n.comment, n.promote, n.moderate, n.sticky, n.tnid, n.translate, r.vid, r.uid AS revision_uid, r.title, r.body, r.teaser, r.log, r.timestamp AS revision_timestamp, r.format, u.name, u.picture, u.data FROM node n INNER JOIN users u ON u.uid = n.uid INNER JOIN node_revisions r ON r.vid = n.vid WHERE n.nid = 1469