Man, Anand, your brain has been working overtime !
1) What is the height difference at the Entry? Usually marble is at a descent height to deal with. Sometimes it's possible to mill up a a profile for a threshold type transition. This can look good, and at the same time ease the height difference.
2) Are you talking about the "sweep" on the bottom of the door? If so... Sometimes you can get away with adjusting them
slightly. But obviously you still want a nice seal at the threshold. If adjustment does not provide an adequate seal, you can either do one of two things. Possibly replace the sweep with a different sweep, that will seal, or,most likely, raise the threshold and adjust the sweep, ( this probably will involve trimming the door ). Oh, and,... Yes metal next to wood is typical. But if you dont like the look, something can usually be figured out using wood.
3) Well, I should have read 3 before 2. Yes, I would do that. It's all engineered to act as a unit, to weather seal. Just make sure when you re-install to seal everything good, with 100 percent silicone.
4) Undercut far enough to allow for expansion. On the "ends", you dont have to be concerned with expansion. If your concerned about creating a "big hole"...You can shoot silicone in there , before you slide the wood under, ( this will seal the hole, and still allow movement).
5) What type of surfaces are you meeting in the doorways ?. You shouldnt have to undercut higher.
6) You can always transition to a slider. There are numerous ways, depending on the situation, a picture would help.
Why do you have to replace the dishwasher? Are you wanting a new one ?
7) I think we need a picture of this, for different options.
8) I use a prybar and a hammer. If the wood is down really tight, I will take a circular saw and cut the floor into a grid pattern.
( Hey Keith, For some reason that "cool face" is coming up when you hit the number eight
. Is that my keyboard taking a dump ?)