I have done what you are talking about on two boats. This is what worked for
me.
1. I used two outlets, one would do but would be hard to arrange the exhaust
ducting in the usually short space between the engine and transom. I would
use two.
2.Usually just above the water line, it ca be partly below but should have
some section of it exposed to air. However, you have to use good judgement
here in assessing the risk of sinking should your exhaust piping become
dislodged from the thru hull. Make sure to use some "Salisbury" type
flappers for backwash and some flooding protection in case of the dislodged
deal above.
3. Yes, on the muffler. From the elbows use a section of rubber exhaust
hose, then for routing the use fiberglass tubing (see west marine catalogue
or other) . For the muffler, I have built a couple of sets out of fiberglass
based loosely on the baffling concept used by Flowmaster, an automotive
performance? muffler.
Finally rubber coupling to the transom thru hulls, use double ss hose clamps
as all joints. I would use 3" system all the way, I think your riser
outlets will be 3" as well. If you fabricate your muffler, you can custom
fit it so that one or two bends in the exhaust ducting can be eliminated.
Best of all is the sound of a lightly muffled V8 that's how a boat should
sound. It was great music for trolling.

For building the muffler, I made a plywood female mold which formed three
sides and allowed me to arrange the baffling easliy before placing the
fourth side on. My mufflers were rectangular in crosssection. I used mostly
CSM and ortho resin. The baffling helps stop the flat sides from druming as
well.
That ought to give you some ideas so you can build your exhaust system. Good
luck.

--
Ron White
My boatbuilding website is:
www.concentric.net/~knotreel