Re: Do I need to still use the Jack Plate?
I could be wrong but it looks to me like your Yamaha is a long shaft (20") motor mounted on a 15" transom. That would explain why you have the jack plate in the first place. When you say long shaft Etec, if you mean 20" shaft, you will need the jack plate again.
Again I could be wrong as it is hard to tell from your pictures, but in the bottom pic your motor looks to me as if it may even be mounted a little low. In the bottom pic it looks like you have some sort of fin mounted on the anti-cavitation plate. It looks to me like it is well below the keel. I don't see the fins in the top pic.
As others have said, when you mount the new motor start with the anti-cavitation plate about even with the keel. The higher you raise it the better your performance will be as long as it stays low enough for proper cooling system operation and no slippage of the prop in turns.