Desktop/Finder won't display external hd's, but will in Disk Utility

Yesterday, I replaced the original hard drive on my late 2008 Macbook Pro (OSX 10.9.4, 2.4 GHz Intel Core 2 Duo processor, 8 GB 1067 MHz DDR3 Memory) with a 1TB SATA hard drive matching the data transfer speeds of the original hard drive.  I backed up via Time Machine (on a 2TB) and even cloned onto a second external hard drive (now called 3TB) and had recovered documents (less than 100GB) from a crashed external hard drive (1TB from OWC brand) onto a third one (now called "1TB portable") with the intent of merging the files from the 1TB OWC crashed hard drive via the 1TB portable back onto an internal hard drive which now had some elbow room.  My problem is that after erasing & restoring the new internal hard drive using Disk Utility & Time Machine and reinstalling Mountain Lion and then Mavericks, the 3TB external & 1TB portable external hard drives went missing on my desktop and on Finder, but were still listed in the sidebar in the "Disk Utility".   Both external hard drives displayed and were able to be browsed through prior to my Time Machine backup & internal hard drive replacement.  Both the 3TB & 1TB portable drives were purchased new and specifically said they were for Mac OS X.  All drives are virus-free and are physically working.  Fortunately, on the 2008 Mac, the new internal hard drive is working beautifully like a brand-new Mac.  Additionally, the 3TB & 1 TB portable are NOT recognizable by other Mac's, but, again, were recognized and operational before I reinstalled OS X ML & Mavericks and restored from Time Machine.  Also, I've set my Finder Preferences to be able to see them.  Both were Mac formatted.  The only additional relevant info I think to add would be that in installing my hard drive, my OSX was Mavericks both before and after and that the Time Machine backup was within within the hour before replacing my hard drive so not much changed there time-wise. Once again, I had verified successful data transfer to the 3TB external & 1TB portable external hard drives immediately before Time Machine backup on the separate third drive.  1) How do I recover the backup data from the 1TB portable drive that I already recovered from the crashed OWC drive and 2) since I was obviously misapplying information from the forums somehow, how should I appropriately clone/transfer data in the first place?  Thank you in advance for your help.

Hi,
I have had a similar problem. I have a 1Tb portable Seagate drive which I have been using successfully for backups with time machine on a Macbook running Lion for 18 months.
I decided to upgrade to Mavericks and experienced the same symptoms as above. The machine would not recognise the disk in finder. Disk utilities could see the disk but the partition was greyed out and several attempts to repair disk were to no avail. I am afraid that I made matters worse by unsuccessfully trying to reformat the disk.
I made a backup of my macbook to another older mac and tried the hard disk with an old Windows laptop running Vista. It recognised the disk but said it need to be formatted. This I did.
In the mean time I had upgraded my Macbook from 10.9.3.to 10.9.4. I am not sure if this made a difference.
I then plugged the hard disk back in to the Macbook. It recognised it immediately and said that it needed initialising. This I did successfully and (MAC os extended Journal). The disk now works perfectly with 10.9.4 on the Macbook and I have been able to use Time Machine with it to make a backup.
I know this does not help with rescuing data from the hard disc but at least I now have a usable hard disk!

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