Arnold... Your set up is going to work AWESOME! Ask me how I know. When you get it buttoned up with the porting and your new head,and proper jetting,you are going to be blown away. I'm running the stock carb and will not be changing it any time soon.
Remember VELOCITY! It crams that crank case full,and makes the engine a snap to tune. Please don't fall for the... "You need a bigger carb" bull s**t. That stock carb will have no problems feeding that ported engine...you'll see.
The advantage to the stock mikuni VM26,is that it fits like a glove from the intake boot,all the way back.
Just make sure to have a hand full of jets on hand when you get it back together. I had to go up 12 to 13 sizes,and I'm at 4,500 feet in altitude. The closer you are to sea level,the more sizes you'l have to go. Your head will be in the mail today.