UPDATE: Today while i was sitting at a light i noticed my battery voltage changing quite rapidly, but still within the limits (not in the red). Could this be a bad alternator or battery/connections.
It seems to follow the noise im hearing from the engine, sounds as if the power isnt being delivered correctly.

I changed my spark plugs and wires and still had 3 & 5 misfire, then I changed all 3 coils and yeah it runs like new.

If coils dont work it could be a bad module.

We try not to suggest shotgunning 3 coils as a troubleshooting step. If a misfire is suspected, swapping coils around, or swapping in one new coil in each location is a much better alternative.

With ignition problems, checking the primary and secondary coil resistances is something easy to do, as is checking resistance of plug wires and inspecting plugs.

Fueling is rarely the issue with these types of problems. Over 95% are ignition related.

Low alternator output can indeed cause low spark voltage.

The o2 sensor is out of the picture when the engine is cold. The computer doesn't use the signal until it goes into open loop operation (warmed). I suspect your coil packs, be sure to clean those two posts when you have one off. Thats the real connection back to the eec. I had a reoccuring misfire on 6 this past winter and thats what cures it, a light sanding of those two posts with very fine sandpaper.