sometimes this is a real PITA
first make sure you are using truck/van engine mount block brackets and that you dont have a car one or pair of them
most likely the way that the hole is not lining up requires that the engine needs to come down further
the only way to get it to do this is to either put one of those factory triangle plate spacers between the block and the bracket, some appplications used these such as some vans, and some cars like firebirds and camaros in the 80s
etc.
sometimes i have had to use none, or one, or a pair
to get the mounts to line up so bolt will go through
trial and error
but make sure you have truck brackets first off, the truck ones have the engine bolt hole farther away from the block, are taller brackets
put them side by side against car ones and youll see this difference,
also i like to take the mounting brackets and get a nice flat file and a nice rat tail file and file all the holes and flat face file the insides where the through bolt goes through, and also the backside of the brackets at the three mounting holes,
to clean them up, sometimes it helps getting bolts through it when installing
good luck
