Yes. No. Maybe. Sometimes.
The auger twist ratio is different and I believe the 6041 is shorter as they have a different angle from the fuel hopper.
The fuel pot for a 6039 won't work without drilling out a hole for the ignitor that the 6039 didn't have. But, having said that I once saw a USSC stove that was identified as a 6041, name plate and all documentation that came with it. It had the square fuel chute like all other 6041's but no ignitor, and the firepot was the same as a 6039.
In some cases you might find a different make of low/high limit switch, no problem they will work, also the vacuum switch might be a different make, again not a problem. I think they just went with whatever could be sourced and met specs.
The fake firebrick will fit from one to another but you need to mod it for either a square auger hole or a round one.
Edited to add. The gear box for the auger motors are a different ratio also. I don't consider that a problem though because you can adjust the fuel feed by pounds per hour in each heat range.
I agree with you Pete.
A few additions I have noticed.
To the best of my knowledge
6041 and 6039 differences
Older 6039s have a 5/4 finger agitator and square ended firepot.
As opposed to later 4/3 finger agitator and angled ends firepot.
The 6041 fire pot is higher on front and sides. (with aforementioned igniter hole)
The augers are different threads. directions and pitch.
AND CONFIGURATION.
6039 is horizontal
6041 is diagonal
6041 is counter clockwise and 1 rpm
same motor as 6039 agitator (stirrer)
6039 is clockwise and 4 RPM
same motor as 6041 agitator
Chain drive and opposing motor position changes CW to CCW agitator direction.
All motors (fans too) are interchangeable with the above considerations.
The complete combustion blower housings are different part number
, haven't tried a swap. Same part numbers on the exhaust fans.
I have been told some US Stove 6039s have the 7 inch exhaust blower .
I have only seen 6 inch exhaust fans
6039 firebrick can be cut for rectangular feed 6041 usage.
Please double check the following
with a Owners manual wiring diagram, and the stove wiring.
I am not responsible for differences I have not experienced.
As far as I know (again my personal experience only)
Wiring is identical. at least ON LATER (2006 +) models I have.
with the exception of an ignitor on the 6041.
As all the diagrams I have checked show the same wiring as on MY STOVES>
I believe Firepot Pete mentioned a difference in wiring to swap an ABC to a 4 button board,
I have been able to interchange them freely.
I am adding inline fuses to my older 6039s (ABC ) for each motor to protect the board.
I used a 6039 to run a 41 with a bad board.
It ran well enough to check the components until I got a board repair.
Big difference I noticed is 6041s and some 6039s have a170F. high limit switch (80390)
the older 6039 has a 250 F. high limit switch. (like Pete said)
Personally I like the 6039 better.
I have bought ,refurbished, and sold both for a few years now.
The auger configuration on the 6041 will jam with too many fines.
Crams the sawdust against the top of the auger shaft and compresses it
Like most newer stoves and all Whitfields.
Bottom feeds being the exceptions, never had one.
WE sieve the bottom 1/8 of the bags on good pellets and more on older or low quality pellets.
Get maybe a handful with fresh bags of high quality.
Not necessary on a 6039,
Some guy on the WEB runs one strictly on sawdust,
has problem getting enough air,
My concern is sawdust is explosive.
I have never gotten a '41 to burn as clean and hot as the '39 I've had for 4 years.
White ash as fine as powder above 3 (of 9) HR.
With high quality pellets.
Could be the high limit ?
I pay good money for old "parts" US Stove 6039s.
OP got a bargain.