You don't really need a row number - nor do you need a break...

Declare @rowsAffected int = 0
  , @batchSize int = 200000   -- adjust for your...

When you test - are you testing with objects that are schema qualified?

SELECT ... FROM myschema.table WHERE ...

Or are you testing by just referencing the table?

Why not just use an inline table-valued function instead of creating a #temp table everywhere?  If you absolutely must have a temp table - you could always select from the...

How are the SSIS packages deployed?  Hopefully you transitioned to project deployment - and deployed to the integration services catalog.  If not - then you need to consider doing that...

You can use OUTER APPLY

FROM tblRemovals r
OUTER APPLY (SELECT TOP 1 DateCleaned FROM tblCleans c WHERE c.SerialNumber = r.SerialNumber AND DateCleaned >= DateRemoved ORDER BY DateCleaned) AS...

There is nothing wrong with having a large transaction log file - and you will need that size when you decide to reindex again.  The number of VLF files doesn't...

What version of Visual Studio did you install?  Did you include reporting servers, analysis services, reporting services and integration services during the installation?  I know that Visual Studio 2015 does...