Based on your TOP, your server is barely being utilized. However, if you are receiving timeouts, you are probably running out of bandwidth. If you are using FDC (which I believe that you are), they do not offer true 100Mbps unmetered servers. Rather, they offer 100Mbps ports on your server and the bandwidth is shared. The average server on their 100Mbps ports sees about 10-30Mbps during peak hours (8:00am - 8:00pm CST GMT-6) and 50-80Mbps off-peak (8:00pm-8:00am CST GMT-6). If you have a lot of visitors accessing your server, it is likely that you are running out of available bandwidth to handle your traffic, hence the timeouts.

Upgrading to a 1Gbps unmetered port will help. However, note that FDC has tiers at the 1Gbps port level. True bandwidth can range from 100Mbps to 1Gbps depending on which level you get.