The reason the bolts do not line up with the bellhousing is because you have a 3 speed mount on a wider 4 speed transmission. It is easy to cut back the mounting points on the bracket to move it over so the bellhousing bolt holes line up. That way the pedals will come through the floor in the correct position also.
That is essentially what the factory did when a 4 speed was used. If in the future you go back to a 3 speed you will need to put shims between the mount and transmission.
I do have plenty of water pump adapters.
