Im sure your organization will be alot more upset when the server decides to take a nose dive without backups or when their crucial data disapears and shows up in the competitions hands, then they would be if you drop the server for a few hours to do this correctly.
You dont want to take chances on mission critical servers. A little downtime now WILL save you a lot of downtime later. spread the work out over a few days.
Run backups one night while no one is working, maybe a weekend. Gather all the software that you will need, find all CD keys, and create backups of your configs for each program.( I swaer there is nothing more frustrating then not being able to find a disk or a cd key when trying to meet a deadline) All of this can be done and the box is still operational. Write down all the IP information, all the little settings that may only take a few minutes to look up but will bite you in the ass when you are rushing to get it back online. Then one night do a differential backup of the box to go along with the full you did over the weekend. Order you a nice pizza, and some caffinated beverage of your choice and spend your night doing the following.
then take the next day off.
Thank you all folks.. for your help.. Yeah XTC I suppose I will have to go for this procedure now. Still learnt a lot from all the recent R & D performed in order to clean. Got some positive results too. But am aware that the packet storm will start again if left alone.
Starting afresh is the only option .. . this week seems going to be verry busy for me now. Anywayz pizza with a bear is something I like most while working late at nights. THe procedure decided and the bash going to kick off. ..