Are you sure its the board and not a head cable? It was working fine before you did the head swap right? Maybe retrace your steps to make sure.
If you change the fuses too, solder on a glass fuse holder (2 wire from the fuse holder to the board) so its easier to change the fuse out if it pops again. You can drill 2 holes in the back of the cover to mount them too and wont have to take the cover off again.