I replaced my alternator and now it's misfiring, does the alternator change the timing at all? 

That should not affect timing. 
 

You’re sure you have an identical match on the alternator ? 

Coil may be loosing its life. 

Alternator has no relation to timing...  and changing timing doesn't usually cause misfires anyway.

Check for damaged vacuum hoses, loose wires, damaged/worn spark plug wires, etc, that may have happened during alternator replacement.

Was an issue with under voltage once the battery was fully charged it went away 

If true, that means you have a *very* marginal ignition system, and probably should check plugs, wires, cap, rotor, etc.