Are you getting any check engine lights at this point? If the distributor is not installed correctly on this one you will get a trouble code for a camshaft/crankshaft position correlation issue. Here is what you need to do to properly setup this distributor with no initial marks on the distributor.
Important: Rotate the number 1 cylinder to top dead center (TDC) of the compression stroke. The engine front cover has 2 alignment tabs and the crankshaft balancer has 2 alignment marks (spaced 90 degrees apart) which are used for positioning number 1 piston at top dead center (TDC). With the piston on the compression stroke and at top dead center, the crankshaft balancer alignment mark (1) must align with the engine front cover tab (2) and the crankshaft balancer alignment mark (4) must align with the engine front cover tab (3).
Notice: The ignition system distributor driven gear and rotor may be installed in multiple positions. In order to avoid mistakes, mark the distributor on the following components in order to ensure the same mounting position upon reassembly:
Notice: Use the correct fastener in the correct location. Replacement fasteners must be the correct part number for that application. Fasteners requiring replacement or fasteners requiring the use of thread locking compound or sealant are identified in the service procedure. Do not use paints, lubricants, or corrosion inhibitors on fasteners or fastener joint surfaces unless specified. These coatings affect fastener torque and joint clamping force and may damage the fastener. Use the correct tightening sequence and specifications when installing fasteners in order to avoid damage to parts and systems.
Tighten Tighten the distributor clamp bolt to 25 N·m (18 lb ft).
Tighten Tighten the screws to 2.4 N·m (21 lb in).
Note the correct orientation of the wire boot.
Important: If the MIL is turned ON after installing the distributor, and a DTC P1345 is found, the distributor has been installed incorrectly.
Yes they are somewhat optional. Are you getting a check engine light? If so have you pulled any trouble codes? Have you checked this engine for vacuum leaks?
Wow that is strange for sure. I cannot say I have ever ran into that before. As far as the #3 miss, you have verified that there are no vacuum leaks that could affect this cylinder. I would recommend checking for spark at the #3 cylinder to verify that you have good blue-white spark at the spark plug. I would also look very closely at the porcelain part of the plug to verify that it has not been cracked for whatever reason.