Mid 2012 MBP Problems after 2nd HD install

So I ordered the following two things:

HGST Travelstar 7K1000
BrainyTrade HDD caddy

I installed them, booted up and decided not to click initialize when the message initially came up. I used disk utility to create two partitions 1 OSX Extended and 1 exFat. It created the partition table fine, but then gave an error while formating the OSX Extended. Since then I have reformated it 1 giant partition. I try to conduct file transfers to it and it seems like there is a 30 second gap where it will do nothing and then transfer 15-25megs and then another gap. I can't seem to figure out what might be the problem or if I missed something.

Any suggestions?

Thank you

niteflyr said:

Some 2012 MBP's had issues with SATA III drives in optibay that was resolved with a firmware update. Make sure you have EFI 2.9 installed.

http://blog.macsales.com/14064-expand-the-2012-macbook-pros-with-an-owc-data-doubler

http://support.apple.com/kb/HT1237?viewlocale=en_US&locale=en_US

Click to expand...

Well I updated the SMC firmware, rebooted and then went back to try to update the EFI however when I open it, it states that it is not supported on my system. I made sure I downloaded the correct version, so I am guessing it is either already running it.

This means it is either the drive or the caddy. I guess tonight I can pull the drive and put it in an external enclosure at test it that way.