Macbook Pro Boot time and general response time slow.

I'm running 10.9 Mavericks.
Yesterday as I was doing my every day activites I realized randomly my macbook pro began preforming extremely poorly.
My problems:
Boot time now takes 2-3 minutes.
Applications take 2-3 minutes to open.
Applications will say they're open sometimes but will not display.
Applications will take several tries to quit.
Applications, especially Safari, will randomly crash.
Everything is slower and takes a while to do, even opening a simple folder will take a minute.
The things I have tried:
I ran a Hardware test and the results showed it is not a hardware problem.
I have reset the SMC and PRAM and the problems still occur.
I have Verified and repaired the Disk/Permissions, however it seems to stop mid-way through (after about an hour).
I can't seem to figure out what's wrong with it. I can re-install the OS but with my internet it is estimated to take 8 hours.
Any suggestions?

Your disk may be failing.  Do not attempt to resintall the OS until your disk is healthy.
Backup your data immediately:
Before proceeding you should make sure you have a current backup.  If it has been getting slower over time your disk could be a failing slowly.  SATA drives have two retry modes: short and long.  They can continue operating as read errors are increasing.  The long retry cycle is very long and can cause significant performance degradation.  If it has started long retries then it is likely to get worse and eventually fail.  SSDs also have a failure mode where the fail slowly.
Time Machine Basics: http://support.apple.com/kb/ht1427
Most commonly used backup methods: 
https://discussions.apple.com/docs/DOC-3045
Methodology to protect your data.  Backups vs. Archives.  Long-term data protection:
https://discussions.apple.com/docs/DOC-6031
Make a Genius Bar reservation http://www.apple.com/retail/geniusbar/ .
or find an Apple Authorized Service Provider https://locate.apple.com/country
If it is a failing disk, consider an upgrade to a 1 TB, 7200 RPM disk. Check out a one terabyte HGST 7K1000 7200 rpm, SATA III drive from OWC or consider an SSD.

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