Rocket stove driving my wife crazy

My Rocket stove is working fairly well, but I have a few problems.
1) I still get a bit of smoke in the room upon lighting and at various times during the burn. My house smells like smoke most of the time if I am using the stove daily. Is there a way to catch the occasional puffs of smoke? I do have a cap which allows air through but makes kind of a chamber which catches a lot of the smoke. Is there a modification on this which would work more efficiently. If I can't fix this, my wife is going to make me take the RMH out in favor of a traditional wood stove.
2) How long should I wait before I do the final sealing layer and what is the best medium for this? I have been using the stove fairly consistently for about a month. It no longer seems wet, but it may be deeper down.
3) The area around the burn chamber gets warm and maintains warmth for at least12 hours, but the bench really doesn't get all that warm. I have about 20 feet of flew running 2 directions through it in an L shape. I also have a bypass which was recommended in one of the posts I read here to use after the burn is out. Is too much escaping this direction past the baffle or am I not burning long enough. I have a hard time getting and maintaining flow through the bench due to the smoke issue mentioned in (1) above.

Hey Tim, what did you end up doing about the chimney situation? The chimney for my RMH (double-wall insulated chimney pipe) goes straight up through the ceiling, attic and roof. The greater portion of the chimney is within the envelope of the house. It has a very good natural draft all year round. I believe this is why my RMH doesn't suffer from smoke back issues at all. But I am careful to open a window a little bit when there is an exhaust / vent fan running somewhere in the house, to prevent it from creating a vacuum that would cause the RMH to reverse draft.

Your bench should be noticeably warm, especially after 3 to 4 hours of burning. If not, then it is probably still drying out. Is your exhaust pipe getting warm? Once the mass is completely dry the exhaust pipe exiting the mass should be just warm to the touch after running the stove for a few hours. And when the bench warms up, the stove will draft even better.

Byron, I have not corrected the flew pipe to double wall and straight up. I will do this next. Can I use galvanize pipe or do I need to go black pipe or heaven forbid stainless? I think you mentioned making my own double walked pipe from 6" insulated inside 8". What do you use for insulation?

Tim, galvanised works all right. Use roxul/rockwool as insulation; it even exists in tube shape specialy for chimneys. And you don't need the outer tube in that case.