Backup and Recovery of Enterprise

Question

I've inherited an instance of Enterprise XI R2, and have discovered that it is a critical system, but is not being backed up.  I'm new to this, please bear with me.
I found the backup and recovery guide (https://www.sdn.sap.com/irj/scn/go/portal/prtroot/docs/library/uuid/c09a069c-6a3f-2b10-3399-e0ed04d866f8), and it gives a good high level overview, but I need a little more info.
Questions: 
1.  The guide states that "The Central Management Server (CMS) and all job-processing and Performance Management servers should be stopped by an automated script."  Is there a specific order that the servers need to be stopped and started in?  Would anyone be willing to share their script?
2.  I assume that when the servers are down, anything scheduled to run during that time will be lost.  i.e., the server won't check for missed jobs caused by the stopped state once the it resumes, correct?
3.  The only thing that I need to back up on the file system is the contents of FileStore (C:Program FilesBusiness ObjectsBusinessObjects Enterprise 11.5FileStore*.*), correct?
4.  This looks like a vanilla install using MySql.  Would anyone be willing to share their MySql backup scripts?  Is there a default password for MySql?  How can I determine this password?  How many databases are there? 
5.  I plan to create a backup script that stops the servers, copies the FileStore path to a backup folder (using xcopy to preserve the archive attribute), have MySql generate a backup file to the same folder, and then start the servers.  This folder will be written to tape nightly (fulls on weekends, incrementals during the week).  Is there anything else that I might need to backup?  Config files?  Ini's?
Thanks!!!

Answer 1

1. There is no specific order, but last to go down should be CMS and first to come up should be CMS.
@echo off
Stop Business Objects Services
echo
net stop "BOBJCrystalReportApplicationServer"
net stop "BOBJEventServer"
net stop "BOBJProgramServer"
net stop "BOBJOutputFileServer"
net stop "BOBJProcessServer"
net stop "BOBJInputFileServer"
net stop "BOBJDestinationServer"
net stop "BOBJCrystalReportspageserver"
net stop "BOBJJobServer_Report"
net stop "BOBJCentralMS"
exit
Similarly to Start services, instead of stop use start and put CentralMS at the top and save it as a batch file.
2. Jobs running when the server goes down will fail, other recurring jobs will wait till the server comes up.
3. Yes, backup File Store & Database.
4. Not sure about the default password for My SQL, you should be able to backup the MySQL database, I have done that once.
5. Backup FileStore & Database.