Secondly, no I didn't do the driver board/ alligator lead test yet because I assumed that being a new board it was more than likely it would be ok, but I will go and check the 3 bank drop targets first and then do the driver check.

I think you'd be better to verify the driver side first, I wouldn't go as far as to say you're crazy if you don't, but ....  It must work for everything else to be ok, it's a pretty quick and easy test that will aide your understanding and allow a decent visual check of the plugs which is also necessary.  Yes, it's a new board, but infant mortality is not unheard of.  If it passes then you have immediately narrowed down your field of search for the problem.

Another thing you can do is with the driver switch matrix connectors removed and the all the drops up. ejects and ball trough empty then use a multimeter to test for continuity between col 1 and each row. Then move to col 2 and again step through each row and so on.  You should see open circuit between everything. Any short circuit is an area for investigation.