Root Server Performance / Tuning

Ich bin mir nicht ganz sicher, aber drupalcenter bietet zu Server-Einstellungen und Konfigurationen recht wenig Auswahl an. Daher hier eine Anfrage, in der Hoffnung, man kann hierbei mir und anderen helfen. Ich weiß ich weiß, das leidige Thema "was man nicht kann, sollte man lassen" aber jeder fängt mal klein an, deshalb hier mal der Root Server den ich betreibe und mit ach und Krach hin bekommen habe.

Ist ein Server mit
festem Arbeitsspeicher 2000 MB
dynamischem Arbeitsspeicher 4500 MB
CPU 1000 MHz
Debian 5.0 / Confixx 3.3.5 Bundle

MySQL-Datenbank 5.0.51a
PHP 5.2.6-1+lenny8
Drupal 6.17
PHP-Speicherlimit 180M
Zend Optimizer / Accelerator / Boost-Modul aktiviert

top Ausgabe
  top - 20:13:18 up 17:25, 1 user, load average: 2.65, 7.92, 11.90
  Tasks: 59 total, 8 running, 51 sleeping, 0 stopped, 0 zombie
  Cpu(s): 57.9%us, 42.1%sy, 0.0%ni, 0.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st
  Mem: 4608000k total, 942960k used, 3665040k free, 0k buffers
  Swap: 0k total, 0k used, 0k free, 0k cached
  
   PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
   5740 www-data 15 0 110m 70m 9m S 33.9 1.6 0:07.28 apache2
  18168 www-data 16 0 98700 55m 9844 R 30.3 1.2 0:01.49 apache2
  25788 mysql 15 0 390m 197m 4836 S 10.2 4.4 34:54.78 mysqld
   5724 www-data 16 0 101m 64m 10m S 6.6 1.4 0:06.71 apache2
  15452 www-data 16 0 81212 42m 10m S 6.3 1.0 0:04.75 apache2
  10190 www-data 18 0 94256 55m 10m R 4.6 1.2 0:06.64 apache2
  15437 www-data 16 0 55344 14m 7872 R 2.6 0.3 0:02.01 apache2

Tunin-Primer.sh
  Uptime = 0 days 4 hrs 16 min 50 sec
  Avg. qps = 513
  Total Questions = 7919442
  Threads Connected = 1
  
  Warning: Server has not been running for at least 48hrs.
  It may not be safe to use these recommendations
  
  To find out more information on how each of these
  runtime variables effects performance visit:
  http://dev.mysql.com/doc/refman/5.0/en/server-system-variables.html
  Visit http://www.mysql.com/products/enterprise/advisors.html
  for info about MySQL's Enterprise Monitoring and Advisory Service
  
  SLOW QUERIES
  The slow query log is enabled.
  Current long_query_time = 2 sec.
  You have 4121 out of 7920180 that take longer than 2 sec. to complete
  Your long_query_time seems to be fine
  
  BINARY UPDATE LOG
  The binary update log is NOT enabled.
  You will not be able to do point in time recovery
  See http://dev.mysql.com/doc/refman/5.0/en/point-in-time-recovery.html
  
  WORKER THREADS
  Current thread_cache_size = 10
  Current threads_cached = 9
  Current threads_per_sec = 0
  Historic threads_per_sec = 0
  Your thread_cache_size is fine
  
  MAX CONNECTIONS
  Current max_connections = 50
  Current threads_connected = 1
  Historic max_used_connections = 38
  The number of used connections is 76% of the configured maximum.
  Your max_connections variable seems to be fine.
  
  No InnoDB Support Enabled!
  
  MEMORY USAGE
  Max Memory Ever Allocated : 2.04 G
  Configured Max Per-thread Buffers : 2.22 G
  Configured Max Global Buffers : 362 M
  Configured Max Memory Limit : 2.58 G
  Physical Memory : 4.39 G
  Max memory limit seem to be within acceptable norms
  
  KEY BUFFER
  Current MyISAM index space = 131 M
  Current key_buffer_size = 320 M
  Key cache miss rate is 1 : 73
  Key buffer free ratio = 82 %
  Your key_buffer_size seems to be fine
  
  QUERY CACHE
  Query cache is enabled
  Current query_cache_size = 32 M
  Current query_cache_used = 19 M
  Current query_cache_limit = 1 M
  Current Query cache Memory fill ratio = 60.09 %
  Current query_cache_min_res_unit = 4 K
  MySQL won't cache query results that are larger than query_cache_limit in size
  
  SORT OPERATIONS
  Current sort_buffer_size = 32 M
  Current read_rnd_buffer_size = 1 M
  Sort buffer seems to be fine
  
  JOINS
  Current join_buffer_size = 10.00 M
  You have had 98 queries where a join could not use an index properly
  join_buffer_size >= 4 M
  This is not advised
  You should enable "log-queries-not-using-indexes"
  Then look for non indexed joins in the slow query log.
  

my.cnf

  basedir = /usr
  datadir = /var/lib/mysql
  tmpdir = /tmp
  language = /usr/share/mysql/english
  skip-external-locking
  #
  # Instead of skip-networking the default is now to listen only on
  # localhost which is more compatible and is not less secure.
  bind-address = 127.0.0.1
  #
  # * Fine Tuning
  #
  key_buffer = 320M
  thread_cache_size = 128
  thread_stack = 128K
  # This replaces the startup script and checks MyISAM tables if needed
  # the first time they are touched
  myisam-recover = BACKUP
  myisam_sort_buffer_size= 64M
  max_allowed_packet= 32M
  table_cache= 12000
  open_files_limit = 32000
  sort_buffer_size= 2M
  read_buffer_size= 2M
  read_rnd_buffer_size= 1536K
  max_connections = 50
  max_user_connections= 600
  table_cache = 500
  thread_cache_size = 10
  connect_timeout = 10
  max_allowed_packet = 16M
  sort_buffer_size = 32M
  thread_concurrency= 4
  max_heap_table_size = 64M
  #
  # * Query Cache Configuration
  #
  query_cache_limit = 1M
  query_cache_size = 16M
  query_cache_type = 1
  #
  # * Logging and Replication
  #
  # Both location gets rotated by the cronjob.
  # Be aware that this log type is a performance killer.
  log = /var/log/mysql/mysql.log

Apache
  #
  # Timeout: The number of seconds before receives and sends time out.
  #
  Timeout 30
  
  #
  # KeepAlive: Whether or not to allow persistent connections (more than
  # one request per connection). Set to "Off" to deactivate.
  #
  KeepAlive On
  
  #
  # MaxKeepAliveRequests: The maximum number of requests to allow
  # during a persistent connection. Set to 0 to allow an unlimited amount.
  # We recommend you leave this number high, for maximum performance.
  #
  MaxKeepAliveRequests 150
  
  #
  # KeepAliveTimeout: Number of seconds to wait for the next request from the
  # same client on the same connection.
  #
  KeepAliveTimeout 2
  
  ##
  ## Server-Pool Size Regulation (MPM specific)
  ##
  
  # prefork MPM
  # StartServers: number of server processes to start
  # MinSpareServers: minimum number of server processes which are kept spare
  # MaxSpareServers: maximum number of server processes which are kept spare
  # MaxClients: maximum number of server processes allowed to start
  # MaxRequestsPerChild: maximum number of requests a server process serves
  
  StartServers 5
  MinSpareServers 5
  MaxSpareServers 10
  MaxClients 40
   MaxRequestsPerChild 8000
  
  

MysqlTuner
  -------- General Statistics --------------------------------------------------
  [--] Skipped version check for MySQLTuner script
  [OK] Currently running supported MySQL version 5.0.51a-24+lenny4-log
  [!!] Switch to 64-bit OS - MySQL cannot currently use all of your RAM
  
  -------- Storage Engine Statistics -------------------------------------------
  [--] Status: +Archive -BDB -Federated -InnoDB -ISAM -NDBCluster
  [--] Data in MyISAM tables: 308M (Tables: 360)
  [!!] Total fragmented tables: 6
  
  -------- Performance Metrics -------------------------------------------------
  [--] Up for: 4h 21m 50s (8M q [514.489 qps], 38K conn, TX: 2B, RX: 1B)
  [--] Reads / Writes: 85% / 15%
  [--] Total buffers: 394.0M global + 45.6M per thread (50 max threads)
  [!!] Allocating > 2GB RAM on 32-bit systems can cause system instability
  [!!] Maximum possible memory usage: 2.6G (59% of installed RAM)
  [OK] Slow queries: 0% (4K/8M)
  [OK] Highest usage of available connections: 76% (38/50)
  [OK] Key buffer size / total MyISAM indexes: 320.0M/131.4M
  [OK] Key buffer hit rate: 98.7% (11M cached / 154K reads)
  [OK] Query cache efficiency: 94.6% (5M cached / 5M selects)
  [!!] Query cache prunes per day: 993457
  [OK] Sorts requiring temporary tables: 0% (0 temp sorts / 19K sorts)
  [!!] Joins performed without indexes: 98
  [!!] Temporary tables created on disk: 49% (2M on disk / 5M total)
  [OK] Thread cache hit rate: 98% (727 created / 38K connections)
  [OK] Table cache hit rate: 49% (498 open / 1K opened)
  [OK] Open file limit used: 82% (877/1K)
  [OK] Table locks acquired immediately: 99% (396K immediate / 396K locks)
  
  -------- Recommendations -----------------------------------------------------
  General recommendations:
   Run OPTIMIZE TABLE to defragment tables for better performance
   MySQL started within last 24 hours - recommendations may be inaccurate
   Adjust your join queries to always utilize indexes
   When making adjustments, make tmp_table_size/max_heap_table_size equal
   Reduce your SELECT DISTINCT queries without LIMIT clauses
  Variables to adjust:
   query_cache_size (> 32M)
   join_buffer_size (> 10.0M, or always use indexes with joins)
   tmp_table_size (> 120M)
   max_heap_table_size (> 32M)

Das sind die Daten die ich zur Hand habe und jetzt auf dem Schlauch stehe, da der Server ziemlich lahm geworden ist, z.T. bis zu mehreren Minuten.
Kann mir jemand dabei helfen, den Fehler zu orten?
Danke