Migrated to an SSD and now windows won't boot properly

It is always recommended to install the OS with no other drive (except optical) in your system. It may be looking to the old drive for the boot partition that normally is created when the OS is installed.

Did you do a complete drive copy or partition copy from the HDD to the SSD?

I used Macrium to copy the entire HDD

Your Best bet is to do a RE_INSTALL, with HDD disconnected (as Elmo stated).
You might try running windows installation disk in upgrade mode, don't think it will fix problem, but only lose 15 min of time.

When going from a HDD -> SSD the recommended method is a Clean Install with the HDD disconnected and the BIOS set to AHCI.

If you must move HDD -> SSD You should NOT do a clone, migration is exceptable and I have used EasyUS and EZ-Gig-IV with no problems.
If you do the Migration, the first thing you should do is disconnect the HDD, connect the SSD and Boot to the SSD to Verify it is working properly, then and only then should you delete your windows OS from the HDD.

Well,

I did indeed end up with a clean reinstall of the OS via a USB stick which I had to create on my mates laptop.

Thanks for your help guys,

Everything is running fine now.

OK - good.
NOW: Do yourself a favour. Go to control panel, backup and create an image of your SSD - It is quick. The image should be saved to the HDD, I also Back up to an external drive.
Should you ever need to re-instal - it's a 15 min job, Select repair, then Repair using image, 15 mins later your back up and running with the system exactly like it was when the image was created.
NO more; re-install windows, Will only down load windows updates that were installed after image was created, No more re-load all drivers, and all programs are there!.