You must replace the throttle body gasket and the upper intake gaskets, they are not re-usable. A leak from an old gasket will cause engine performance problems at idle and through the rev range and may be compensated by the PCM adding extra fuel that will damage the CATs.
Use new replacement gaskets, they are not expensive.
Do you know what the flat labor time is to replace all 6 spark plugs? I am getting different responses from different shops. They range from 2.0 hours to 3.5 hours. What is reasonable? Did not get to it this summer and it's too cold in New England now for me to want to take this job on myself.
I don't know the Ford spec rate, but I would suspect that 2 hours labour is more than enough for the V6. Removing and replacing the upper intake is easy for a tech and they do it all the time on those 3 liter V6 and the later ones in most of the Ford line of transverse engined cars. I looked at some estimating sites and 2 hours seems to be a good number.