Server running very slow

About 6 hours of the day my server runs really slow. It has 1400 accounts but only about 300 are really active. and the server sometimes runs steadily smoth at 0.20 cpu and 40% memory. here is my top output. If anyone can tell me a better way to troubleshoot the cause of my server load, ide greatly appreciate it. Whats WA stand for? its at 94% that cant be too good.

Code: 
top - 09:39:15 up  4:13,  1 user,  load average: 44.63, 41.80, 31.81
Tasks: 267 total,   1 running, 261 sleeping,   0 stopped,   5 zombie
Cpu(s):  2.3% us,  3.0% sy,  0.0% ni,  0.0% id, 94.5% wa,  0.2% hi,  0.0% si
Mem:    506496k total,   493036k used,    13460k free,     6780k buffers
Swap:  1015800k total,   504572k used,   511228k free,    50188k cached

  PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND
  206 root      15   0     0    0    0 D  1.0  0.0   8:02.62 kjournald
16091 root      16   0  3932 1064  744 R  1.0  0.2   0:00.48 top
16105 fire271   18   0 14608 3968 2192 D  1.0  0.8   0:00.63 cpanel
16144 root      18   0  8716 3356 1336 D  1.0  0.7   0:00.07 pureauth
16100 root      16   0     0    0    0 D  0.7  0.0   0:00.05 pdflush
   43 root      15   0     0    0    0 D  0.3  0.0   0:28.49 kswapd0
 8682 nobody    15   0 29328  15m 2024 S  0.3  3.1   0:02.34 httpd
 8683 nobody    15   0 32688  19m 2064 S  0.3  3.9   0:02.01 httpd
 8763 nobody    15   0 32208  15m 2116 S  0.3  3.2   0:01.52 httpd
 8764 nobody    15   0 31468  15m 2012 S  0.3  3.1   0:01.87 httpd
 8844 nobody    15   0 29324  15m 2016 D  0.3  3.1   0:01.46 httpd
10488 nobody    15   0 29796  15m 2052 S  0.3  3.2   0:00.88 httpd
13786 root      18   0 24908 3328 1452 D  0.3  0.7   0:01.68 whostmgr2
14527 root      18   0 24908 3872 1488 D  0.3  0.8   0:01.15 whostmgr2
15578 root      18   0 23344  19m 8456 D  0.3  4.0   0:00.55 whostmgr2
15814 nobody    15   0 32600  16m 1936 D  0.3  3.3   0:02.06 httpd
16043 mysql     18   0 45428 7668 1288 D  0.3  1.5   0:00.41 mysqld
16099 mysql     15   0 45428 7668 1288 D  0.3  1.5   0:00.04 mysqld
16137 deepak    18   0 14608 3968 2192 D  0.3  0.8   0:00.03 cpanel
    1 root      16   0  2264  448  420 S  0.0  0.1   0:13.26 init
    2 root      RT   0     0    0    0 S  0.0  0.0   0:00.21 migration/0
    3 root      34  19     0    0    0 S  0.0  0.0   0:00.02 ksoftirqd/0
    4 root      RT   0     0    0    0 S  0.0  0.0   0:00.40 migration/1
    5 root      34  19     0    0    0 S  0.0  0.0   0:00.02 ksoftirqd/1
    6 root       5 -10     0    0    0 S  0.0  0.0   0:01.74 events/0
    7 root       5 -10     0    0    0 S  0.0  0.0   0:01.15 events/1

 

 

 

 

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