Here the situation I just finished putting my motor make together while its in the car. All I have left to do is install the distributor but for some reason the rotor will not point directly at the #1 cylinder like it should according to the hayes manual. The timing mark is at 0. I've done this twice before without problems but now it just doesn't want to align right. I tried turning the motor over when it was close to aligning but all I get are backfires through the TBI. The spark plugs are all in the right place on the cap and engine.
Suggestions?

Would improperly setting the valve lash cause something like this.

 

Does the distributor drop all the way down until it is flush with the intake manifold?

If so, then all you need to do is lift the distributor just enough to rotate the rotor one tooth and that should being the rotor and #1 cap terminal into alignment.

Be aware that is will cause the oil pump drive to be mis-aligned with the distributor drive, so you'll have to either use a long screwdriver to reach in and turn the oil pump drive or just sit the distributor down as far as it will go (it won't drop flush with the intake) then bump the engine until it drops down fully.

I use the bump method because it's easier than pulling the distributor, turning the oil pump rod, reinstalling the distributor only to have to pull it to make another adjustment to the rod.

Hope this helps.

Jake