Junk Rules Run Now: very slow

Question

My computer crashed over Xmas. I had to get a new one because an electrical surge earlier in the year caused a small unknown problem that became a big known problem. I had all the backups. I had some issues between IMAP and POP mail that I resolved by going POP so I could combine all my email addresses into one PST file on drive not "C" as I had before the crash.
For a few months while I was restoring all the other non-MSFT software, I had several email files for each email address I have. That created many duplicates. I was able to remove most of the duplicates using PST Tools. Its toolset could not filter many duplicate emails; however.
So, I bought the tool that ExtendOffice had via a link to 4Team that removed quite a few.

I imported all my standard built-in Outlook rules that send emails to specific folders. The other day I imported the ExtendOffice rules that find junk emails. Because it took so long to rebuild my computer (tax season and more), I have 6,000 emails (according to the folder count) to filter for junk. It runs VERY, VERY SLOWLY.

Why? Other than trying to avoid such a conglomeration of emails, can the junk filter run faster?

BTW: What is the syntax for tags on this site?