2002 A6 avant 3.0 just started acting strange. Runs smooth for the first 20-30 secs. then cel starts flashing engine running rough and these are the codes i pulled off the car P0300 Random multiple misfire, P0304 and P0303 cylinder 3and 4 misfire. was going to take a look at the plugs butnot sure of the cylinder locations. Can someone help or tell me what could cause this or were to start.

 

Check plugs, coil packs and fuel filter. Never worked on the 3.0, but man I am sure you can find the plugs if you just look... They could be hidden under some plastic covers like the 2.7t's are. Good luck!

 

deffinitly check the amps as well. the amps are located on top of your air box (i think on a 3l)

best way to check and see if it is the amps is to switch the amps around. ie. put the left one on the right ad the right one on the left. them check to see if the miss fire codes are on different cylenders.

 

On the 3.0L the power output stage in built into the coil pack so there is no "amp" like twinturbomew said, the 3.0L coil packs are just as bad as the 1.8T coilpacks and are replaced on a daily basis for falling apart to just plain causing multiple miss-fires. I can almost gaurantee the two coil packs are bad.
How you number any audi V6 engine is 1,2,3 passenger's side front to back, then 4,5,6 front to back driver's side. Since you have misses on cylinder 3 and 4 you want to check the second and last coil pack on the driver's side. Try swapping the coils to other cylinders then clear the fault codes and see if the miss-fire moves to another cylinder.
NOTE: for the 2.7T swapping coil packs won't help you diagnose miss-fires because the power output stage is seperate.

 

For the 2.7T, if you swap the coil packs and the misfire follows the pack, doesn't that isolate the fault to the coilpack, instead of the POS?

 

If you swap the coil to a different cylinder and the miss-fire follows the coil on a 2.7T itDOES mean the coil is bad. But since the 2.7T coils have an external power output stage or ICM (on the air box) the chance of this happening is slim to none. I would say about a 5-8% chance of a failed coil on a 2.7T and a 90% chance on a 3.0L engine. Note that the manufactures of these coils are different and the company that makes the coils for the 1.8T, 3.0L, and 4.2L engines have had a track record of failures by either the coil coming apart at the center, or a complete dead miss in the cylinder like the spark plug was never there. On the older 1.8T engines with an external ICM the part that commonly fails is the ICM not the coil, thats just how it is on audi's.