Thanks Phil. I did end up fixing it.
I pulled the MC out to test it and it was fine, so put it back in and tried bleeding again with no success.
In the end, I got a small plastic funnel and put it upside down on the MC bottle and then stuck my compressed air blower in the end of the funnel and gently put air pressure into it and it forced the fluid through the line and took the air bubbles with it.
This worked very well though you need to be VERY careful not to release too much air as it will blow the fluid everywhere.
The other option is to use a vacuum bleeder, which is effectively the opposite of what I did to bleed it. Bleeding the traditional way just doesn't work.