LOL, this is pretty stupid but I realised why I had had so much trouble with the end game.

I did finally complete the last section, looks like it was a classic case of just needing a break to get the brain in gear.

Then in a casual conversation with a friend at work he mentioned about the weapon upgrades, then it clicked at no point did I up grade a weapon. How stupid is that probably very lucky to have got to the end game let alone completing it :-)

Right so next time I upgrade any and everything :-)