Hopefully, you have a Honda shop manual to refer to. The carbs for that have several vacuum and fuel hoses etc on the rear as well as the front of the bank. If you do not put them on correctly, it will not run right.
Sounds like something is restricting air. When you remove the enrichment needle, it allows more air to enter the system. If it enters into the top carb, it will go to all the rest.
So check the hoses. Also, make sure you put the intake manifold gasket , muffler plate gasket and the carb base gaskets on correctly.
I highly recommend purchasing the Honda Marine Carburator Manual
http://www.helminc.com/helm/product...=&from=result&Style=helm&Sku=TM044&itemtype=N
It goes into nausiating detail (with colored pictures) as to how all of the Honda Carburators work. It has a section for those with thermal enrichment valves...including the 30 - 50 HP. It also has trouble shooting guides. It shows how the fuel is supposed to flow at start, idle, acceleration and full throttle. It shows basically a road map of fuel through the carbs. Nice to know, when you are trying to clean them and do not know where all the passages are.
I still refer to it when there is an unusual situation. I learn something everytime I look at it. Or maybe it is just my bad memory and I keep learning the same thing over and over again.....ground hog day".
Mike