Transferring HD data - Time Machine vs. Bootable Clone

I'm upgrading the HD on an old MacBook Pro (3+ years old) to a SSD drive.  But I'm going from 500 GB to 240GB.
I originally was going to move some files off to an external drive but I kept getting ".DS Store file" messages.
So now, I'm considering selectively restoring from a clone or a Time Machine.  Does it matter which one?
Also besides the .DS_Store file, here ae some othe issues that have crept in over time: 
1)     My Mail program was running a 40 minute delay for a week or so after installing Mavericks, until Mail stopped working entirely.
2)     My Photo Library has been mangled at least once and haven't been able to restore it completely.
3)     I don't know if this is normal or abnormal, but over 2 apple laptops, and 5-6 years, I've 6-8 external/internal HDs have died.  The last one was my Time Machine Backup, 2 months ago.  I haven't been doing anything that intensive, I'm not usually a game player and I'm usually pretty good at properly ejecting the external HDs.  I was able to test 6 of the failed HDs when a friend lent me A friend recently lent me a SATA to USB cable.  Plugging the HDs directly into the computer, 5 of 6 drives were functioning, but only 2 of them had usable data.  I've already erased and repurposed one to temporarily act as a Time Machine backup.
Do I have too many errors floating around in my Libary, User,Permissions, etc? 
Am i better off doing a selective installation from Time Machine, a Clone or starting from scratch with a new copy of Mavericks, restoring apps and files bit by bit whatever I can?
Thanks,
Joel

Gentlemen,
                 Thanks for all your great advice. 
The ".div_Store" error messages, the bad Photo Library, and current Mail issues have me concerned with possible errors in Permissions, User, Library files.  I'm a total novice at this, I make no claims to understand code or the intracicies underneath the hood of my machine.  Maybe I'm being naive or just paranoid about some of these issues I've experienced, but these files have been through 10+ years of OS upgrades and at least 3 different computers.  Maybe there has been a clean install or two along the way but something is going on.
I'm concerned with deleting original files, especially with this ".div_store" error message.  Every copy has the chance of error even if it's small and there already is some error creeping in.  I can perserve the original disk, along side the clone and the Time Machine Backup and do a selective install.
And if I'm willing  take my time, I can test all the different possibilities.  I've got the original disk, and a clone and a TM backup.  I can test them both the TM & the clone, and see how any of the selcted files do after installation. 
Heck, after a clean install, I could even start from scratch pull software off old disks, from the Apple Store, etc. and reinstall only the 1/2 dozen programs I really use.  I've got way too many programs and files, I never use.  It's great to have them available but they are not needed.  Before I can try copying current files I really need to the cloud, and test whether the ".div_store" issue comes up going to cloud or bringing them back.  If I take my time and make sure I've got apps, programs, files, passwords I need I should probably be able to create everything I need  from scratch.
It's not the fast way, but I've got a computer that works, slowly but it works, so I don't need to rush  I can test a clone or TM first,.  And I've perserved the original and leave open the possibility of even rebuilding from scratch if need be.
                Thanks again to all,
                              Joel

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