Windows 10 extremely long boot after cloning new SSD

For Christmas I got a new SSD. So to move my windows 10 system to the the new hard drive I cloned it and used a system recovery disk to put in the commands to fix a broken MBR. It then booted fine but had a huge in-cress in boot time. This comes from a 20 second boot time from my HDD to a 2+ min boot time for the SSD. The incress takes place after BIOS and it is when the windows logo is shown. Any help would be appreciated.

It doesn't make a lot of sense.

It is possible that you have a borked drive, but typically that would result in read errors. It is possible you are getting those, but it's fixing them each time you power on.

I would recommend a clean install.

If you are determined to fix this version, create a boot log and see what it says.

source: http://pcsupport.about.com/od/commands-s/a/startup-settings.htm

Tap or click on the Start button.
Tap or click on Settings.
Tap or click on the Update & security icon, near the bottom of the window.
Choose Recovery from the list of options on the left of the UPDATE & SECURITY window.
Locate Advanced startup, at the bottom of the list of options on your right.
Tap or click on Restart now.
Wait through the Please wait message until Advanced Startup Options opens.

Enable boot logging

The Enable boot logging option starts Windows 10 or Windows 8 normally, but also creates a file of the drivers being loaded during the next boot process. The "boot log" is stored as ntbtlog.txt in whatever folder Windows is installed on, almost always C:\Windows.
If Windows starts properly, take a look at the file and see if anything helps with the troubleshooting of whatever issue you're having.
If Windows does not start properly, choose one of the Safe Mode options and then look at the file once Windows starts in Safe Mode.
If even Safe Mode doesn't work, you can restart into Advanced Startup Options, open Control Panel, and view the log file from there using the type command: type d:\windows\ntbtlog.txt.