I did it, but it was no doubt a great deal easier as it was new construction.  I have a cabin with a wood stove in the basement.  You use the "black pipe" to the ceiling of the basement, then have to transition to the stainless triple wall.  It goes out the roof and must be a bit higher than the peak of your roof.  It's about $125 for each three foot section and you can't get "L's" so you pretty much have to go straight up through each floor and attic.  

Just go talk to a place that sells it--they will have complete information and codes.  The newer wood stoves are HIGHLY efficient--but expensive--and very safe.  As long as you meet all codes, most insurance companies don't care about them.  If you don't meet code, they will drop you if they find out, or refuse to pay after the house burns down.  Meet all codes--but they are all straight-forward and just common sense.  Good luck.

ETA:  The triple wall pipe only needs 2" of clearance to flammable stuff, so that helps a lot.