Finally got my KZ400 to start! But........

No a smaller one but i think you have a basic problem with your carb set up.
Check your pilot and main jet size.
Some picture of your carb environment will help us to solve your problem.
As i say, one picture says more than thousand words.

would I have to change both pilot and main jets?

Give us first a status of your jet size,(pics will help).
Go here to check your technical data.

www.kz400.com/TechnicaldataFrameset.html

Here are some pictures. But it starts up again. But this time the RPM rises up to 4000 - 5000. is that bad?

This explain your problem.
You are not using the right carburetors = (2-Stroke Engine)
Your new Mikuni carburetors need a single throttle cable each.
You have to adjust the throttle cable in the 2 in 1 connector that both carb slider bodys are lifting sync when you pull throttle.
I am right with your carb setup?

I do have a 2 in 1 connector throttle cable.Would I have to switch to single cables? I thought we use the 2 in 1 connector cables for the mikuni's? I think the carbs are for 2 stroke engine. It is what other people use on their kz400. Also is there any carb intake manifold rubber boots that fits on the my mikuni vm30's and a kz400? With that high of an RPM could there be an air leak?

I do have a 2 in 1 connector throttle cable.Would I have to switch to single cables?
No,you can go with this setup but you have first adjust the wire length on both carb top adjust screws to get a sync movement and exact gap (passage opening) of the carb slider bodys. (remove the idle adjust screws first for exact bottom adjustment )
Sorry if my poor English knowledge sound strange for you but it is the best explanation i can do for the moment.

Michael

It's been awhile. But I have changed the sparks plug, rode around the block for a bit with no choke. Then I realize that one side of the bike runs lean and the other side of the bike run rich. How could this happen?