Can't reset permissions

[EricHawkinson]

CPU
GenuineIntel, Intel(R) Core(TM)2 CPU 6420 @ 2.13GHz
Version
Parallels Plesk Panel v10.4.4_build1013111102.18 os_CentOS 5
OS
Linux 2.6.18-238.19.1.el5PAE

Symtoms:
Last week I started noticing a few of my domains taking forever to load. Sometimes it takes several minutes before I can SSH or FTP in also. When I do get in SSH and FTP there are problems. I can't upload or download files. I can't run some commands when I log into SSH.

I can log into CP and when I go to file manager I can navagate just fine... but when I go to upload a file

Unable to upload <FILE> to //: filemng: Error occurred during /bin/cp command.

So I went to check the error_log

stdout:
chmod: cannot access `/var/www/vhosts/MYSITE.net///FILE.zip': No such file or directory
filemng: Error occurred during /bin/chmod command.


stderr:
filemng: Error occurred during /bin/chmod command.

file: /usr/local/psa/admin/plib/Service/Agent/Transport/Local/Exec.php
line: 98
code: 0
trace: #0 /usr/local/psa/admin/plib/Service/Agent/Transport/Local.php(58): Service_Agent_Transport_Local_Exec->process(2, Object(Service_Agent_Command_Exec), Object(Service_Agent_Log), Object(Service_Agent_Transport_LocalTransaction))
#1 /usr/local/psa/admin/plib/Service/Agent/Transport/Local.php(24): Service_Agent_Transport_Local->_command(2, Object(Service_Agent_Command_Exec), Object(Service_Agent_Transport_LocalTransaction), Object(Service_Agent_Log))
#2 /usr/local/psa/admin/plib/Service/Agent.php(133): Service_Agent_Transport_Local->process('02d255239c617e1...', Array, Object(Service_Agent_Log))
#3 /usr/local/psa/admin/plib/Service/FileMng.php(130): Service_Agent->commit()
#4 /usr/local/psa/admin/plib/FileManager.php(247): Service_FileMng->putFile('/tmp/phpwdPmp8', '/var/www/vhosts...', 644)
#5 /usr/local/psa/admin/plib/ui_common/FileManagerUIPointer.php(510): FileManager->putFile('/tmp/phpwdPmp8', '/var/www/vhosts...', 644)
#6 /usr/local/psa/admin/plib/ui_common/FileManagerUIPointer.php(115): FileManagerUIPointer->_uploadAction()
#7 /usr/local/psa/admin/plib/UIPointer.php(595): FileManagerUIPointer->accessItem('POST', NULL)
#8 /usr/local/psa/admin/htdocs/plesk.php(45): UIPointer->access('POST')
#9 {main}

It looked like a permissions problem so I thought I would try and reset them.

but then I found that I could run a reset
# /usr/local/psa/admin/bin/httpdmng --reconfigure-all
This resulted in

bash: httpdmng: command not found

I went to the bin folder and a found that
all the files the bin folder have "-> ../sbin/warpper" next to them and I can't access any of them.

This is where I have hit a wall.