I am making an eclosed porch into a bathroom with a tub, toilet and lav. My question is being that this is a enclosed porch with a crawl space below it can I cut through the sill plate to run the 3 inch line to connect it to the main?

Yes you can. But don't butcher it. Cut about 3 1/2" wide opening, just to fit the pipe. Cut all the way though. ( Pipe is 3 3/8" O.D. and mud plate is 3 1/2" wide ). Once the pipe is in, nail approved nail plates over the hole, preferably from both sides. These plates are Heavy Duty gauge and are 1 1/2" x 12". They accept 4 - 16 penny nails on each end. These plates not only protect pipe from nails but also hold the mud plate together.