You are welcome for the links. I keep them handy. 😉
I don't envy you in trying to clean this one up. It is a long and painful road for sure. I have had the "pleasure" of cleaning up many of these types of queries in the past and it generally requires a lot of time and effort to unravel everything and get it right. Even harder when the logic from the original is suspect.
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Need to split a string? Try Jeff Modens splitter http://www.sqlservercentral.com/articles/Tally+Table/72993/.
Cross Tabs and Pivots, Part 1 – Converting Rows to Columns - http://www.sqlservercentral.com/articles/T-SQL/63681/
Cross Tabs and Pivots, Part 2 - Dynamic Cross Tabs - http://www.sqlservercentral.com/articles/Crosstab/65048/
Understanding and Using APPLY (Part 1) - http://www.sqlservercentral.com/articles/APPLY/69953/
Understanding and Using APPLY (Part 2) - http://www.sqlservercentral.com/articles/APPLY/69954/