Brief Run down of my car:
04' MT 79K miles/highway driven RB Duct, B&B midpipe, 3" Magnaflow exhaust, new OEM coils/wires/plugs EDIT: Latest flash was also done around 4K miles ago.

Just recently aquired an AP underdriven pulley from a buddy. Installation went smooth but after the install I got the P0300 - Random Multiple Cylinder Misfire and P0301 - "Cylinder" One Misfire codes. Seemed kind of odd to me getting those codes since I just changed coils/plugs/wires about 4k miles ago and hadn't had any issues or CELs other than the no CAT deal from the midpipe.

While driving at speeds of 25-45mph the CEL illuminates and blinks for several seconds(scanner picks up codes above during this time), and then it goes out while cruising at highway speeds. I have ZERO drivability issues. No studdering, no lack of power, no odd noises, just that pesky light saying there is a misfire. I can even lay into the throttle and the car performs like it were brand new.

I've checked the following and all is O.K.:
Spark at each coil/plug while idling
crank trigger wheel for bent teeth
power at each coil
resistance at each coil
resistance on wire leads
swapped coils/wires with someone else
Reset ECM using the pedal method and disconnecting battery with no luck.
Put factory pulley back on = no problem

Odd misfire codes went away when I swapped back to the factory pulley. That's the fix for now, but I'm still curious as to what a simple pulley change could have done to cause this. I'm a well educated ASE certified tech, but this ones got me. Any one else have a similar issue or suggestion?

This is not a very "odd" occurrence and a search would have resulted in many threads with the same issue.
You need to perform a reset after the installation:
1) Turn the key to 'ON' (not start)
2) Press the brake pedal rapidly until the oil pressure gauge needle sweeps half way and back down.
3) Turn the key to the 'OFF' position.
4) Start the car.

This is not a very "odd" occurrence and a search would have resulted in many threads with the same issue.
You need to perform a reset after the installation:
1) Turn the key to 'ON' (not start)
2) Press the brake pedal rapidly until the oil pressure gauge needle sweeps half way and back down.
3) Turn the key to the 'OFF' position.
4) Start the car.

Did that... no luck.

Saw a thread with similar issues here http://www.rx8club.com/showthread.php?t=179055 , and his fix was disconnecting the battery, which also yielded no positive results. I'll add them to my things done list. I'll try again anywho. Thanks.

You mentioned:
Put factory pulley back on = no problem
So if everything runs OK with the stock pulley, don't waste your time checking everything like the coils, plugs, or positioning plate because everything works fine stock.
Did the oil pressure needle sweep during the 20x brake stomp reset?

You mentioned:

So if everything runs OK with the stock pulley, don't waste your time checking everything like the coils, plugs, or positioning plate because everything works fine stock.
Did the oil pressure needle sweep during the 20x brake stomp reset?

Put the factory pulley back on after I had checked all that stuff looking for any issues with the AP unit in place. Yes, needle did sweep back and forth when I tried the reset procedure.

For a free part, and a measly gain in performance, it's likely I won't try and reinstall it for the sake of going through similar quirks. If I do in the future I'll try the reset again. I'm aware there are several threads pointing to the reset, but obviously it hasn't worked in my favor. Who knows... all is well in factory trim for now.

Thanks for the help and instruction. I'm not so much "rotary" inclinded as I am with piston motors.

The pulley really isn't worth the trouble (or money).
I would just stick with the stock one.