For Q 1 and 2...

You can script all objects including database using EM without any problem..

Q3 and 4:

Restore msdb on to...

did you try changing the distribution agent profile?

http://msdn2.microsoft.com/en-us/library/ms152515.aspx

Peer to Peer transactional replication...

http://searchsqlserver.techtarget.com/tip/0,289483,sid87_gci1133488,00.html

I agree with you SSIS is completed for simple task to provide complete ETL tool...

Did you try SQL server Object transfer task in SSIS?

Right click on databases/Restore database/Click radio button FROM FILE/Click ... button/Click Add on SPECIFY BACKUP window/

Bottom of the Locate backup window...Replace the file path with your UNC path and enter...

As Sugesh mentioned use db mail and see the following article

http://www.sqlservercentral.com/columnists/cBunch/introtodatabasemailinsql2005.asp

For sql mail error check the following article...

http://support.microsoft.com/kb/223877

I setup the db mail on many servers some of them are RTM and SP1 but not on SP2 without any problems...

Installed on test server...I didn't get any issue with installation...

You can't to logshipping or restore to sql 2005 from 2000.

It is one way traffic...

You can go to 2000 to 2005 but not 2005 to 2000

I believe you can stop sql server to on secondary server and copy the .ldf and .mdf files to the other location and restart the sql services...

I think your dbs...

In SPECIFY BACKUP window click Add botton at the bottom you see the SELECTED PATH which you can overrite it.

Looks like to me it is MemToLeave memory issue...

If you restart sql services this will be fixed if it is memtoleave memory...

If you can efford few seconds down time, restart...

How to impede Windows NT administrators from administering a clustered instance of SQL Server

http://support.microsoft.com/?id=263712

Yes, you can replication procedure definations...

See BOL for more info and read the following article..

http://searchsqlserver.techtarget.com/tip/0,289483,sid87_gci1241182,00.html

Can you please post your backup and restore commands as is... just change the db name...