I know this is off-the-wall Pete, but your motor looks tilted up farther than normal. Maybe it's just the height of the brackets throwing my perspective off, and I don't have one in mine right now to go out and compare to, but it all looks tilted farther than I remember.
Is that possible in your case? If other things have changed, maybe someone here could compare theirs to yours, say the valve cover angle to the fender, maybe that would tell the tale.
See? I said it was off-the-wall and a long-shot. Unless you put some odd type of trans and mount in there and it's too low, or there are some uber-tall engine mounts in it, I don't see what else would cause that (other than my crossed-eyes that is!).
Unless you don't have a trans in it at all yet? That would be too much to hope for, I'm sure, but it's worth a mention.
And back to the pump, obviously there's no way to get the pulley on wrong-way-round, so is it possible that there are pulleys with different offsets? This pulley came with the kit I presume, but maybe someone here with an '89 Mustang setup can compare.
You're correct about them (usually) being seated to the end of the shaft, but they usually don't have that much of a gap between the pump body and back of the pulley either. They can be pushed a bit past the end of the shaft in some cases (tools allowing), but I don't think there's enough there to be the answer.
With the P/S kits though, you sometimes have to space the pump back off the bracket to fit. There to too many different pumps that people can use (we've run afoul of that here many times!), so there is that to wonder about too. But here again, that's a lot of spacing, so not sure.
Which exact pump are you using, and why is not spacing it back an option? Will the tank hit the engine, or the tank inlets interfere with the fender? Kind'a looks that way from here, but the angle is not good to see that.
We had a bracket go out defective recently (documented here on CB) and had to replace it due to some incorrectly fabbed components.
It wasn't just bent (which is usually easy to fix) but had at least one, if not two, little tiny threaded bosses welded on completely crooked. Unfortunately for our customer, it wasn't caught at the manufacturer and got boxed up and sent out for him to discover when his pump didn't line up.
Not saying that should make you happy about yours, or make it any less of a hassle to deal with. Just that it has happened to us too.
Don't mean to muddy the waters, but I'm throwing out things that look to be possible help. I hope!
Good luck.
Paul