cowboy,
Back to basics, try bringing the engine to TDC. on #1.
then pull the cap and see what post on the cap the rotor points to.
This is assuming that you have #1 on the compression stroke.
If you don't know, spin the motor with the starter after you have pulled the #1 plug, put your finger in the hole and when the piston blows air or your finger out of the hole you're right there.
notice the timing mark on the balancer it should line up with the timing tab or real close anyway. You might have to move it back in line with the mark, when it is that will be TDC. #1.
Use that post for #1 in your firing order or pull the distributor and turn the to the post you want to use as #1. Just leave the motor alone, don't let it move and you'll be fine.
On a side note, if the timing is right and all is correct, then you have an issue with the dead cylinder causing the miss.
BRANT