Alternator issues with indy heads

Here is a pic with the bolt problems ...it is a 408 with indy heads. The bottom bolt of the swing arm that goes into the water pump is 3/8" gap ...if I tighten it...the swing arm starts to bind up against the alternator. The second problem is with the bolt that goes through the alternator to the head. It also has a 3/8" gap and cannot put the spacer in between the ears of the alternator. Both gaps are 3/8" ...belt looks lined up. Is a power mater square back alternator in a 3-wire.