Does it hurt to use Throttle body cleaner to clean out the upper and lower intake I have both off the engine and want to get them as clean as I can.

 

No it shouldn't hurt at all. I've used brake parts cleaner on them before. It is aluminum I am assuming.
I use the TB cleaner first. Then with all of the plastic parts removed, I use aluminum wheel cleaner (acid type for etched, non coated wheels). This makes the aluminum look brand new. (I wouldn't do the wheel cleaner thing if your intake as some kind of coating on it though.)

 

What Brand of Alumium cleaner would you recommend? I was Planning to paint the lower and upper intake