Ok so I found a 100% sure way of stopping ALERTs and only the alerts you want to stop.
First thing I did was stop the Immediate Alert Timer job waited to make sure it wasn't waiting to run 1 more instance.
now any task you create or edit that will send out an alert will get cached. This is when you open up your SQL Server Managment studio and connect to the content database of the sharepoint site the alerts are on.
In the EventCache table any row that has the columns [EventData] and [ACL] not = to NULL will send out alerts for that item. So by doing some simple SQL querys like
SET [EventData] = NULL
,[ACL] = NULL
WHERE [EventTime] > '2010-10-11 00:00:00.00' AND [ListId] = 'LIST ID HERE' AND ModifiedBy = 'USER DOING THE MODIFY HERE'
will kill all alerts from a certain time onward and on a certain list and modified by a certain user. After you kill all the alerts turn on the Imediate Alert Timer job and no alerts will be sent out.
Of course you can always modify the SQL query with different criterias to meet your needs.