yes, as Ganoid said and speaking under the assumption that the timing mark on the crank is showing TDC, ignition timing is only a matter of cam position, not the crank position. there is only up or down for the piston. compression or exhaust stroke is controlled by valve position.

a quick question -- before you started messing with it, was your timing showing correct or was it always screwy? not sure if this is possible, but I read once that the actual pulley can rotate on the balancer, though I'm not sure how, or whether that's even possible on ours, but all else being correct, that may explain the 45* or 90* off.

BUT, everything being okay, it's not probable for your timing to be that far off without overlooking something somewhere.

go over it again.
rotate your crank to TDC.
pull the valve cover and look at the cam again to make sure it's in the proper position, as well -- timing mark just left of the 12 o'clock position.
then install the distributor.

if it's still off at that point, I'd look at how you're installing the distributor, because you're most likely off a couple of teeth.

the way I install the distributor is to kinda eyeball and line up the the middle of the slot with the bolt hole. then I rotate the rotor to around vertical and put it in. when it rotates to the left, it's right about at the #1 position. this should put you right where you need to be.