Hi Jason! Warm welcome to the rocket scientist corner of the internet.
For starters, an excellent resource for answering a lot of your questions can be found in the
Rocket Mass Heater Builders Guide by Erica and Ernie Wisner. Loaded with pictures, tips and advice from those that have built a lot of stoves and share what they have learned.
Jason LaPort wrote:Does the exhaust pipe out have to be the same size as the pipe going in?
Yes. To keep it simple, all cross sectional area from feed to exhaust needs to be the same except for the manifold area which is the transition from the barrel to the mass.
Does the exhaust going out of the stove need to be higher then the feed tube?
Usually it ends up being lower but then it goes (relatively) straight up and generally a few feet above the roof peak.
I kinda want to build a 3in system for now and over the summer work on making a larger and more efficient system.
It has been suggested many times and by many people that the smaller you go in size (than a 6" system), the harder it is to make the stove run properly and cleanly.
Poke around the
Rocket Mass Heater forum and look at some of the builds that others have done. Lots and lots of information that can keep you busy for a while.
Good luck with your build and do post pictures when you begin so we can see what you have and help you out easier.