VC Vigilant, can't shut down without puffing, random puffing otherwise.

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I have really struggled with the Vigilant and this house, I replaced my old Vigilant(1979 short door) with a fresh one this year, the Vigilant I am using is a 1983 2 piece back model, it was fully dismantled, cleaned, reassembled with furnace cement, new gaskets, etc. yes I have read the manual front to back several times and have been using a Vigilant for my whole life, I will be 40 next month. I am burning mostly Ash, Maple, and Oak that has been split for 3 years, stacked and covered for 2. the chimney is a 7x11 rectangular flue with a flexible liner, so probably 6x10? and 31' from the thimble to the top ( yes it is very tall), I am heating a 2400 square foot log cabin build in 1977, its tight as log cabins go, but it is not a super tight house by any means. The issue I have is that I cannot get this thing to idle, theoretically I should be able to burn it in updraft mode, ( damper open, secondary air closed) and just use the primary air supply to regulate the fire, this is not the most efficient way to run the stove, but I should be able to do it. If I close the secondary air supply and close the primary, before long it begins to puff, and flip the primary flapper open, sometimes it even lifts the griddle. It will do likewise in horizontal burn mode (damper closed). My solution to prevent the puffing, smoking and sucking has been to bend a small piece of copper wire into a U shape and put it in the primary air opening so the flapper can't completely shut , this works well, but it will allow the stove to over fire unless you close the damper, even then sometimes we get what I guess could be considered a small chimney fire going where it burns off any excess creosote in the stove and stove pipe, it will run hot, 7-800 degrees for a period of time maybe as much as an hour, but usually it settles down after half an hour, I clean my chimney every year, and sometimes if I feel it needs it I bought one of those flexible rod with nylon string attachments for a drill with 30' of rod. I can pull the stove out and run it right up the thimble, I get a lot of sooty stuff and a few crumbles, but nothing you would call an excessive creosote buildup. Something I did do recently was to seal where the oval adapter goes into the cast throat, by checking around the stove with a lit long nose lighter I determined it was sucking a fair amount of air in through that joint, still even tonight, with a 350 degree stack temp and maybe an hour and a half into a horizontal burn, it decided to give a good puff, I opened the top and rearranged the wood inside and let it heat up a bit, so far its behaving again. this behavior is something I have struggled with for quite a while.
My dad has a Defiant Encore and an Encore that will go indefinitely just simmering along in updraft without ever engaging the damper. why am I struggling so hard with this Vigilant?

Any input here would be appreciated, I have considered making an adjustable disk with a small, maybe 5/16 hole, installed on the primary flapper so I can regulate the amount of bypass air that can get by even with the damper closed, I have also considered making something that would work like a valve in an ICE engine where as it pulled hard for air the valve would open allowing a small amount by. I feel like it is trying so hard to suck air through any orifice that it is literally pulling the damper door shut where it can't open even if it needs to until it finally manages a small explosion inside and then it pops the door open and takes a gasping breath.
 
Sounds like you have too much draft, can you put a key damper in the stove pipe to slow it down a little?
Why do you want to run in updraft mode? You are meant to shut the damper once the flue is warmed up, so do that.
Fire choked down too much or too quickly will puff back, so perhaps you need a small shim to prop the air intake, but just the right size so as not to over fire the stove... Or, experiment with turning it down slower, AFTER you shut the damper..... Good luck
 
Sounds like you have too much draft, can you put a key damper in the stove pipe to slow it down a little?
Why do you want to run in updraft mode? You are meant to shut the damper once the flue is warmed up, so do that.
Fire choked down too much or too quickly will puff back, so perhaps you need a small shim to prop the air intake, but just the right size so as not to over fire the stove... Or, experiment with turning it down slower, AFTER you shut the damper..... Good luck
I've been shimming the primary air open with the little piece of wire, it works, but still the lack of ability to shut the stove down fully concerns me. The Vigilant has always been a finicky stove in my experience, the one I grew up with was, and this one is, I put one in at my dad's in what is now the office and it putters along just fine. I have wondered if part of the issue here is the super short stove pipe, I littleraly had to cut the compact adapter down to get a 90 degree elbow to work, then so is 2 back to back 90 degree turns right out of the top of the stove, my parents stoves all have 3-4' of stove pipe before entering the chimney, one is horizontal, the other vertical. I have considered moving the thimble up and over to the next flue which could gain me 18" vertical and probably 16"horizontal, the trouble is with that, which is also the trouble here, that I am adapting to a 7" wide tile with an 8" thimble on the side. not my idea of a preferable scenario, but I didn't build the chimney.
The original stove that was in this place was a monstrous Frontier, and it was a bit shorter than the Vigilant and had room for a stove pipe damper. This stove should't need one, and I would prefer to not have one, harder to clean and just a creosote trap.
 
Whether or not you need a flue damper is more dependent on the chimney than what stove you are using. It sounds like your chimney is pulling an exceptionally strong draft and that is contributing to your trouble controlling the stove. Not saying that is the only factor. Having an installation with a couple of bends and horizontal runs would slow the draft down a bit as well.