MacBook Pro :: MBP Slow Bootup & Running?

I have a 2007 Santa Rose MBP and it has started to run very slow during the bootup and actual use of it. Here is how the bootup goes:

I turn it on and get the bong sound and a full white screen. In about 10 seconds I get the Apple log and in about another 10 seconds the circle that rotates as it boots up.

Then at about 2 minutes it changes color to a light blue color with the pointer on the screen. Then in about another 10 seconds changes to a darker shade of blue. At a total of 3 mins and 40 secs I then get the desktop with the space type background and in a couple more seconds the Mac OS X login screen. It takes around a minute until I am able to type anything. For awhile before that time I can type I get the beachball.

Here are the details of what I recently did:
I had a 250GB hard drive in my MBP running the newest version of Leopard. I was down to around 50GB free so I purchased a 640GB hard drive. I also was due to upgrade to Snow Leopard. I had an external USB enclosure that I could temporarily use. What I did is put the 640GB hard drive in that external enclosure and formatted it with the GUID partition table. I then used SuperDuper to mirror my internal hard drive to the external hard drive. I have a lot of programs installed and a lot data on my hard drive so didn't want to lose any of this.

Once the mirroring of my internal hard drive was completed to my external 640GB hard drive I then booted from that drive (using it externally and selecting option at bootup). Things seemed to run fine with no issues.
I then after booting up from this external hard drive did a Snow Leopard upgrade to this external hard drive. Once again this external hard drive appeared to run perfectly normal.

After things seemed to be okay I then opened up the MBP and swapped hard drives so the 640GB drive was my new internal HD. I then booted and once again I used it some and things appeared to work normally.

After this later in the evening I installed two programs, Final Cut Studio 3 and Logic Studio 9. As far as I can remember my computer was acting a little odd and after a reboot that is when all the above issues started.

As far as I can tell this never started until those two installs. Is it a chance I didn't try it out enough but I remember even with the HD being external USB my system appeared to run faster than ever. I even think the program didn't start with Final Cut Studio but started with Logic Studio 9

Any idea of what caused this? Even after my computer running it's VERY slow to the point of being almost unusable. For example if I open Word it takes 3 minutes or so to open. Almost any action causes the beachball to appear.

After looking at the Apple site I did both a PRAM erase (using Command Option P and N) and also a SMC reset by removing the battery and power cord and pressing the power button for over 5 seconds and neither fixed it.

I opened up Disk Utility and did a Verify Permission and got the following information:

Permissions differ on "usr/share/derby", should be drwxr-xr-x, they are lrwxr-xr-x.
Warning: SUID file "System/Library/CoreS...as been modified and will not be repaired.