I dont have a napoliean pellet stove, too expensive for my blood but it sounds to me like you have insufficient outside intake air to the combustion chamber.
How long is the run of the outside air kit. If it is over 3 ft, you should be using 4 inch diameter tubing instead of 2 inch diameter because the longer tube restricts the air flow, which is pulled in by suction, and results in not enough air into the firebox.
My pel-pro 55,000 btu pellet stove has a rod that attaches to a choke plate in the 2 inch cold air intake tub. If I push it all they way in, it closes off 7/8 th of the air & my stove has a lazy,dirty,sooty flame and makes clinkers in the fire pot. if I pull it out,it opens up the cold air supply & I get a hot ,long dancing flame, which gets longer,cleaner , hotter & brighter the further open I pull the air intake conrol rod. Too much cold intake air popcorns the pellets right out of the firepot and onto the steel interior floor of the stove, which be cleaned at keast once a month.
CLINKERS ARE 1/2 way burned pellets all stuck together to themselves and the fire pot screening plate by the tar & creasole created in partial , too rich (not enough air) combustion.
Not enough air can be caused by improper setting of intake air control, ashes in the ash trap under the fire pot, because the ash trap on many models of pellet stove is part of the air path
from the combustion chamber to the exhaust fan blower.
In other words, the ash trap under the fire pot is the suction air intake of the exhaust blower & must be kept clean of too much ashes.
The entire stove works on suction, the exhaust blower only blows out through the exhaust vent pipe that goes through the wall behind the stove.
Anything that cloggs that suction path will cause lazy flames , black window & ashy firebox, maybe some small portion of smoke into the stove room.
Your stove may or may not have a preset air intake adjustment for high & low fires or may have a manuel control as mine does.
So you have to check the suctionpath from the exhaust blower, back through the ash trap and then the fie pot and then through the cold air intake pipe to the back of the stove & then thru the cold air intake pipe to the outside of the house.
Also take the vent hood off & check the interior of the vent pipe for any obstructions,
When you told me the stove ran better when you removed the outside air intake pipe, I know right then you had bad air frow through the conbustion chamber & will find a partial blockage some where, even if it is an improply set intake air adjustment control.
Try reading the owners manuel & back here to see if someone more knowledgeable that me answers your post with specific info of your model stove.
Failing that, ask for a troubleshooter factory rep and ask him what he thinks it is.
Dont let him buffaalo you into a service call unelse you really want one.
They all get quite pushy when they smell money.
I hope this helps you some. too tired to keep eyes open; zombie need coffee!!