For a flowmaster 40 series muffler with single inlet and dual outlet, what is the inlet size and outlet size? Is it 2.5"?

 

Welcome ! Your factory muffler is 2.5" in and out. If you're hooking up your factory intermediate pipe, your muffler will need a 2.5" SI. Since your dual outs will be aftermarket, you can choose the size. 2.25" DO's are typical. So, 2.5" SI/ 2.25" DO.

 

so would a 1999 SuperCrew 5.4 be the same pipes as the original posters truck???

 

Yes, 2.5".