There's a few things that it could be, the first two things that come to mind would be statistics and what's called parameter sniffing.

Statistics play an important part...

Restoring a backup from a 32 bit install to a 64 bit install shouldn't be a problem, I've done that myself a number of times during upgrades like this.  You...

We have a fairly standard process, separate environments for development, quality assurance. user acceptance, production, and appropriate approvals between each level, with a change management meeting occurring before UA things are...

you can do an UPDATE with a JOIN in it like it shows in this link:
https://msdn.microsoft.com/en-us/library/ms177523.aspx#OtherTables

it's hard to tell without knowing what the source tables structure is and the data in them look like.  Is the MRN number what relates these records together?

maybe a database level DDL trigger like this?

CREATE TRIGGER audit_Security_events ON DATABASE --ALL SERVER --DATABASE
    FOR GRANT_DATABASE, DENY_DATABASE, REVOKE_DATABASE
AS
DECLARE @event xml, @subject...

I'm not sure what you mean by 2 parameters, it looks like your dbo.Log procedure has 6 parameters.  You'd probably want to call this in some kind of TRY-CATCH block, such...

Unfortunately the easiest way to look at this is using the old sys.sysindexes catalog view which has the rowmodctr column.  SQL Server won't automatically update statistics until 20% + 500...

I don't know if you can get an e-mail at the time when a permission change happens, I've created reports before using the default trace like the following code:
[code...

how about doing something like this?

DECLARE
    @BeginDate DATETIME = DATEADD(wk, DATEDIFF(wk, 0, GetDate())-1, 0),
    @EndDate DATETIME = DATEADD(wk, DATEDIFF(wk, 0, GetDate()), 0);
...
WHERE...

Index maintenance such as rebuild or reorganization will both contribute to transaction log file growth:
https://blogs.msdn.microsoft.com/timchapman/2012/09/28/index-rebuild-vs-reorganize-the-transaction-log-edition/
How are you performing your index maintenance?  Hopefully something like the free scripts...