MBP slow bootup & running VERY slow

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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.

Since it said it didn't repair it I did a Repair Disk Permissions but that didn't seem to fix it.

Could these two issues be the problem and if so how can I fix them?
Thank you for your help.
 
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Your Mac's Specs
Back to my old 2.2GHz C2D MB after selling my MBP and wondering what my next Mac will be :)
These 2 are to be safely ignored...
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.

As for FCS
Final Cut Studio/Express: Compatible versions for Mac OS X v10.6 Snow Leopard

Can't tell you about Studio 9... or at least before getting more info....
Specs... HD size (inc. space left), Ram, anything else you can add without me asking a plethora of questions :)
 
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I checked and the version of Final Cut Studio I'm using is Snow Leopard compatible.
I am glad those two issues aren't causing the problem since it doesn't seem to want to repair.
I have around 420GB free on the hard drive and 4GB of memory so I didn't think that would cause the problem.
 
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Your Mac's Specs
MacBook Pro 1,1 2Ghz 2GB Ram 120GB HDD
maybe a clean install will solve your issue? kind of a hassle though
 
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You are probably right.i don't want to have to go that route but it may be quicker than figuring out this issue.
 
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You are probably right.i don't want to have to go that route but it may be quicker than figuring out this issue.

my macbook pro was basically acting up, slow boot up time and slow opening apps. i ran permissions and onyx, nothing worked. i didn't have a whole lot of files i needed to back up, i think my music took up like 11gigs of space and that was the main thing for me, all my other apps were downloadable or i had the cds. now it's like brand new fast.
 
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I'm not sure what happened but I ended up doing another Disk Utility on it and it started working now. I had done the same in the past with no luck so maybe I just did something differently this time but fortunately after about a day it still seems to be working. Thank you to everyone for your help.
 

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