OS X works perfectly fine on external HD but extremely slow with HD on MBP
If both the HDD and the SSD are running significantly faster when installed in the external enclosure rather than the internal bay, your SATA cable is likely the culprit. Both should run faster when connected via the internal SATA bus vs external USB 3.0 bus. You can run the Apple Hardware Test (which doesn't test your drive, but does test the connection), but it's prone to false negatives. 

If you are close to an Apple Store, my advice would be to take it in for a free diagnostic (AppleCare won't cover the cost of replacing the cable since you already swapped out the drive, however). At any rate, you can get a definitive diagnosis and then decide whether to go through Apple, use a third-party service, or a DIY solution as posted in the link above. BOL.